Showing papers in "Soil Biology & Biochemistry in 2021"
TL;DR: In this paper, the authors synthesize data on the contribution of plant and microbial-derived compounds to stabilized SOM, i.e., aggregates and mineral-associated organic matter (MAOM), and review the role of environmental factors influencing this contribution.
Abstract: Soil organic matter (SOM) represents a major reservoir of stored carbon (C). However, uncertainties regarding the composition and origin of stabilized SOM hinder the implementation of sustainable management strategies. Here, we synthesize data on the contribution of plant- and microbial-derived compounds to stabilized SOM, i.e., aggregates and mineral-associated organic matter (MAOM), and review the role of environmental factors influencing this contribution. Extrapolating amino sugar concentrations in soil based on molecular stoichiometry, we find that microbial necromass accounts for ~50% (agroecosystems) or less (forest ecosystems) of the C stabilized within aggregates and MAOM across studies. This implies that plant biomolecules, including lipids, lignin, and sugars, might account for a substantial portion (≥50%) of the organic matter protected by minerals and aggregates. Indeed, plant-specific sugars and lipids can each account for as much as 10% of organic C within mineral soil fractions, and most reported quantities of plant-specific lipids and lignin in mineral soil fractions are likely underestimates due to irreversible sorption to minerals. A relatively balanced contribution of plant and microbial biomolecules to stabilized SOM in aggregates and MAOM is inconsistent with recent suggestions that stable SOM is comprised mostly of microbial compounds. Land use and soil type appear to profoundly affect the contribution of plant and microbial compounds to stabilized SOM. Consistent with studies of bulk soils, favorable conditions for microbial proliferation in grasslands or fertile Chernozems or Luvisols appear to increase the contribution of microbial compounds, while less favorable conditions for microbial proliferation in forest soils or Podzols/Alisols appear to favor the abundance of plant compounds in stabilized SOM. Combined with a tight link between substrate quality and the abundance of microbial compounds in stabilized SOM, and a potentially inverse relationship between substrate quality and the abundance of plant compounds, these results provide evidence that plant biomolecules might be preferentially stabilized by organo-mineral interactions in some ecosystems. Various areas warrant further research. For example, difficulties in distinguishing direct and indirect effects of temperature and precipitation on the composition of stabilized SOM may be overcome by long-term observational studies that include climate manipulations. Knowledge gaps in the contribution of plant and microbial compounds to stabilized SOM in soil layers below 30 cm depth may simply be closed by extending the sampling depth. Moreover, a refined focus on soil fauna, with potentially strong effects on microbial and plant compounds in stabilized SOM, will provide new insights into SOM dynamics. Future studies should quantify both microbial and plant biomolecules in mineral soil fractions to allow direct comparisons and overcome limitations in existing data. For example, because biomarker-based estimates of microbial-derived C can only indirectly estimate the maximum amount of plant-derived C, exhaustive studies of plant biomarker concentrations could be conducted, including estimates of plant-specific lipids, sugars, and lignin (and biomarkers released following mineral dissolution). Generally, more integrative studies, e.g., combining molecular and isotopic tracers of organic matter inputs with targeted sampling of mineral fractions, are required to improve knowledge of the formation and persistence of stabilized SOM.
678 citations
TL;DR: In this paper, the contents of fungal and bacterial necromass were estimated based on glucosamine and muramic acid contents in cropland (986 samples), grassland (278 samples), and forest (452 samples).
Abstract: Despite the recognized importance of the contribution of microbial necromass to soil organic carbon (SOC) sequestration, at a global scale, there has been no quantification for cropland, grassland, and forest ecosystems. To address this knowledge gap, the contents of fungal and bacterial necromass were estimated based on glucosamine and muramic acid contents in cropland (986 samples), grassland (278 samples), and forest (452 samples) soils. On an average, microbial necromass C contributed 51%, 47%, and 35% to the SOC in cropland, grassland, and forest soils, respectively, in the first 20 cm of topsoil. The contribution of microbial necromass to SOC increased with soil depth in grasslands (from 47% to 54%) and forests (from 34% to 44%), while it decreased in croplands (from 51% to 24%). The microbial necromass accumulation coefficient (the ratio between necromass and living microbial biomass C) was higher in soil from croplands (41) and grasslands (33) than in forest (20) soils. These results suggest that the turnover of living microbial biomass is faster in grassland and cropland soils than in forest soils, where the latter contains more partially decomposed plant residues. Fungal necromass C (>65% of total necromass) had consistently higher contributions to SOC than bacterial necromass C (32–36%) in all soils due to i) a larger living fungal biomass than bacterial biomass, and ii) fungal cell compounds being decomposed slowly and, thus able to persist longer in soil. The ratio of fungal:bacterial necromass C increased from 2.4 to 2.9 in the order of croplands
420 citations
TL;DR: Plastics accumulating in the environment, especially microplastics (defined as particles) are identified as a major threat to the health of humans as mentioned in this paper, and they are removed from the environment.
Abstract: Plastics accumulating in the environment, especially microplastics (defined as particles
404 citations
TL;DR: In this paper, the authors provide recommendations to more effectively guide and improve how microbial information could be used to yield relevant and actionable assessments of soil health, and discuss some of the broader issues associated with their use.
Abstract: Healthy soils are critical to the health of ecosystems, economies, and human populations. Thus, it is widely acknowledged that soil health is important to quantify, both for assessment and as a tool to help guide management strategies. What is less clear is how soil health should actually be measured, especially considering that soil health is not exclusively a product of soil physical and chemical characteristics. Given their well-established importance to many aspects of soil health, microbes and microbial processes are often used as metrics of soil health with a range of different microbe-based metrics routinely used across the globe. Unfortunately, it is our opinion that many of these pre-existing microbial measurements are not easy to interpret and may not necessarily provide credible inferences about soil health status. Here we review the microbial indices used to assess or monitor soil health and discuss some of the broader issues associated with their use. We provide recommendations to more effectively guide and improve how microbial information could be used to yield relevant and actionable assessments of soil health.
304 citations
TL;DR: In this article, the effects of two microplastics, conventional non-degradable high-density polyethylene (HDPE) and biodegradable polylactic acid (PLA), on maize growth and arbuscular mycorrhizal (AM) fungal communities in a soil spiked with or without ZnO NPs were studied.
Abstract: Emerging contaminants such as microplastics and engineered nanoparticles (NPs) have become an environmental issue of global concern, but little is known about their joint effects in soil–plant systems. We studied the effects of two microplastics, conventional non-degradable high–density polyethylene (HDPE) and biodegradable polylactic acid (PLA), on maize growth and arbuscular mycorrhizal (AM) fungal communities in a soil spiked with or without ZnO NPs. HDPE and low–dose PLA promoted plant growth, while high–dose PLA significantly decreased maize shoot (by 16%–40%) and root biomass (by 28%–50%), indicating high-dose PLA may have strong phytotoxicity. ZnO NPs displayed non-significant effects on plant growth, but caused greater Zn accumulation in plants. Both HDPE and PLA further increased Zn concentrations in roots, while decreasing Zn translocation to aerial parts. High–throughput sequencing showed that microplastics and ZnO NPs singly and jointly influenced AM fungal community composition and diversity, particularly the relative abundance of dominant genera. The presence of ZnO NPs and microplastics generally increased soil pH. Overall, our findings imply increasing contamination by microplastics and NPs can have profound ecological impacts on plant fitness, plant quality, and soil microbial community composition and diversity, resulting in uncertain consequences for agroecosystems.
237 citations
TL;DR: Overall, this study shows that land-use alters the composition and network structure of soil microbiota that determine the litter decomposition, and reveals that specialized keystone taxa are involved in the decomposition dynamics, and highlights an opportunity of harnessing such taxa for manipulating lignocellulose decomposition in soil ecosystems.
Abstract: Plant litter decomposition in the soil is governed by microorganisms such as bacteria and fungi that colonize lignocellulose residues during the decomposition process, and thus, the interplay of bacterial and fungal communities can yield insight into the lignocellulose decomposition dynamics Previous studies have mainly investigated litter decomposing communities in microcosms or ex-situ conditions or at a single soil ecosystem Here we conducted a 12 week-long litter decomposition experiment to explore how the temporal dynamics of soil enzyme activities and microbial communities are linked to litter decomposition under three different land use sites (forestland, farmland, and abandoned farmland) in Nanjing, China We found that litter decomposition in the forestland was the highest among the three land use sites Then, using a multifactorial approach, we showed that this higher decomposition rate in forest soils is determined by microbial communities with higher ligninolytic enzyme activities, higher diversity, and a less complex but more specialized network Chryseobacterium in bacteria, and Fusarium, Aspergillus and Penicillium in fungi were the keystone taxa in networks across three land use types We conducted subsequent culturing that further confirmed the strong decomposition ability and enzyme activities of these taxa, indicating their importance for microbial litter decomposition As such, this is one of the first studies to validate the role of keystone taxa for litter decomposition, and it demonstrates that co-occurrence network scores can be used for statistical identification of putative keystone taxa for further screening and linking to microbiome functioning Overall, we show that land use alters the composition and network structure of soil microbiota that determine the litter decomposition Our study also reveals that specialized keystone taxa are involved in the decomposition dynamics, and highlights an opportunity of harnessing such taxa for manipulating lignocellulose decomposition in soil ecosystems
186 citations
TL;DR: In this article, the authors used 16S and ITS rRNA gene sequencing to detect bacterial and fungal communities and used FAPROTAX and FUNGuild database to predict bacterial and functional groups.
Abstract: Clarifying the response of soil microbial communities and their potential functions during succession is of great significance for understanding the biogeochemical processes and the sustainability of forest development. However, the study of microbial community dynamics during the process of succession remains poorly understood in boreal forest ecosystems. Thus, in order to study the dynamics of microbial diversity caused by succession, we adopted the "space instead of time" method and selected four habitats in a national natural reserve (including grassland, birch forest, mixed forest and larch forest) to represent the primary successional sequence of the boreal forest. We used 16S and ITS rRNA gene sequencing to detect bacterial and fungal communities and used FAPROTAX and FUNGuild database to predict bacterial and fungal functional groups. The results showed that forest succession significantly changed the community composition of bacteria and fungi, among which the fungal community was more sensitive to the changes with successional stage. The relative abundance of ectomycorrhizal fungi significantly increased with succession, while the relative abundance of bacterial functional groups involved in the nitrogen cycle did not change significantly, indicating that fungi might play a major regulatory role in the nutrient cycling process during the successional process. In this study, the soil total carbon and total nitrogen were the dominating factors affecting the soil microbial community and the structure of fungal functional groups. Our results suggest that the shifts in fungal community structure and functional groups may play a key role in soil nutrient cycling during boreal ecosystems succession.
175 citations
TL;DR: In this paper, the authors conducted a global meta-analysis based on data collected from 237 published papers to explore the effect of multiple global change factors (elevated carbon dioxide (eCO2), warming, elevated nitrogen addition (eN), wetting-drying cycle, drought, decreased precipitation (precipitation(−)), and increased precipitation(+)) on microbial diversity across different ecosystems (cropland, grassland, forest, shrubland, desert, wetland, and tundra).
Abstract: Soil microbial diversity is one of the key factors affecting the structure and function of the belowground ecosystem; yet, little is known about the response of microbial diversity to multiple global change factors. Here, we conducted a global meta-analysis based on data collected from 237 published papers to explore the effect of multiple global change factors (elevated carbon dioxide (eCO2), warming, elevated nitrogen addition (eN), wetting–drying cycle, drought, decreased precipitation (precipitation(−)), and increased precipitation (precipitation(+))) on microbial diversity (Shannon index) across different ecosystems (cropland, grassland, forest, shrubland, desert, wetland, and tundra). Global change decreased soil bacterial and fungal diversity by an average of 2.9% and 3.5%, respectively. For each global change factor, the effect sizes of precipitation(−), eN, wetting–drying cycle, and drought on soil microbial diversity were negative, whereas the effect sizes of eCO2, warming, and precipitation(+) were positive. This phenomenon was driven by changes in mean annual temperature (MAT) and edaphic factors (especially soil pH, bulk density and organic carbon content) rather than mean annual precipitation. Moreover, the effect size of soil microbial diversity linearly declined with increasing MAT, suggesting that microbial diversity was highly dependent on climate conditions at the global scale. In addition, two- and three-way interactions of global change factors aggravated the negative effects of individual effects. We suggest that it is essential to conduct long-term, multiple-factor experiments to assess the response of soil microbial diversity to global change because multiple global change factors often occur simultaneously.
157 citations
TL;DR: It is highlighted that soil aggregation stratifies soil nutrition and microbial functional diversity, which leads to the differentiation of aggregate ecosystem multifunctionality, whereas soil traits have more standardized total effects than functional diversity.
Abstract: Soil stability and aggregates are important drivers of soil fertility and microbial diversity and are highly vulnerable to land degradation. However, the role of soil aggregates in driving the responses of microbial functional diversity and multiple ecosystem services and functions (multifunctionality) to further degradation (e.g., fertilization) remains largely unexplored and poorly understood. In this study, we used soils from long-term experiments involving inorganic and organic fertilization treatments to investigate the role soil aggregates (microscale) play in driving microbial functional gene diversity (via GeoChip) and the activity of multiple extracellular enzymes in an agricultural ecosystem. We found that microbial functional gene diversity has a significant and positive relationship with soil multifunctionality, which is enhanced in soil aggregates by organic fertilizer but is reduced by inorganic fertilizer. We also found that soil aggregate fractions indirectly controlled multiple ecosystem functions via changes in functional diversity. Smaller soil aggregates with higher resource availability (carbon and nitrogen) supported more ecological functions than larger aggregates under contrasting fertilizer management regimes. Soil multifunctionality is regulated by the differences in resource availability and not by microbial functional gene composition, which suggests that microbial functional diversity contributed more to multifunctionality than gene composition. Random forest analysis and structural equation modeling indicated that soil carbon and nitrogen and microbial functional diversity together determined the multifunctionality, whereas soil traits have more standardized total effects than functional diversity. Our study highlights that soil aggregation stratifies soil nutrition and microbial functional diversity, which leads to the differentiation of aggregate ecosystem multifunctionality.
142 citations
TL;DR: The term Glomalin-related soil proteins (GRSPs) as mentioned in this paper was originally used to describe a hypothetical gene product of arbuscular mycorrhizal fungi (AMF) that was assumed to be a nearly ubiquitous, thermostable and highly recalcitrant glycoprotein, deposited in soils in large amounts, and deemed to indicate soil health and quality.
Abstract: The term “Glomalin” was originally used to describe a hypothetical gene product of arbuscular mycorrhizal fungi (AMF) that was assumed to be a nearly ubiquitous, thermostable and highly recalcitrant glycoprotein, deposited in soils in large amounts, and deemed to indicate soil health and quality. It was defined operationally as the fraction of soil organic matter (SOM) extractable by a hot citrate buffer and assessed either by Bradford assay or by cross-reactivity with monoclonal antibody MAb32B11. Later, it was recognized that the extracts contained a variety of compounds, including some of non-AMF origin, cross-reactive with both Bradford assay and the monoclonal antibody. This led to re-describing the pertinent (and still only operationally defined) SOM as “glomalin-related soil proteins (GRSP)”, albeit without any substantial change in the underlying concepts. Consequently, a great deal of confusion in this area arose among researchers in soil, plant, and environmental sciences. Glomalin or GRSP (often used interchangeably) has previously been linked to various soil features, including stability of soil aggregates, size of soil C and N pools, sequestration of heavy metals, and alleviation of various plant stresses. GRSP concentrations in soil often, but not always, have been correlated with AMF biomass measured by alternative (mainly microscopic) approaches. GRSP formation, deposition, and/or decomposition in soils seem to be largely dependent on a multitude of interactions among plants, AMF, and other soil microorganisms, including prokaryotes. The chemical structure of GRSP extracted from soil remains unclear and generally complex. That is due to the unspecific mode of its extraction and purification, as well as the great variety of analytical approaches that have been used heretofore to assess it. Future research needs to elucidate the exact composition of this operationally defined SOM fraction, the controls over its production and accumulation in soils, and its exact role in soil ecology generally and soil food webs in particular. Furthermore, novel and independent tools should be established to more specifically (as compared to current glomalin assays) assess AMF biomass and functioning in roots and soil and its involvement in soil processes.
139 citations
TL;DR: In this article, a meta-analysis of 355 observations from 71 studies worldwide was conducted to explore the global patterns and associated drivers of soil organic matter decomposition and terrestrial carbon cycling, concluding that nitrogen (N) and nitrogen plus phosphorus (NP) addition significantly decreased PE, whereas phosphorus (P) addition had minimal effect on PE (P < 0.05).
Abstract: Priming effect (PE) induced by inputs of fresh carbon plays crucial roles in soil organic matter decomposition and terrestrial carbon cycling. Priming effect is considered to be largely influenced by nutrient availability, but the global-scale patterns reflecting how nutrient addition affects PE and the controlling factors for such effects remain unclear. By conducting a meta-analysis of 355 observations from 71 studies worldwide, we explored the global patterns and associated drivers of PE responding to nutrient addition. Results showed that, overall, nitrogen (N) and nitrogen plus phosphorus (NP) addition significantly decreased PE, whereas phosphorus (P) addition had minimal effect on PE (P > 0.05). The effects of N and NP addition on PE varied with ecosystem, experiment and carbon substrate types. Specifically, N and NP addition generally decreased PE in forest and grassland, but did not change PE in cropland. Among experiment types, such negative effects occurred in incubation experiments, but not in pot experiments. Between carbon substrate forms (i.e., containing the added nutrient or not), N and NP addition only decreased PE in groups of carbon substrates that did not contain the added mineral nutrient. Moreover, the effect of N addition on PE depended primarily on the N limitation of microbial respiration across sties, with such effect increasing significantly with microbial N limitation (indicated by microbial respiration response to N addition and C:N imbalance between microbes and resources). Based on this relationship, we proposed a conceptual model linking microbial N mining and stoichiometric decomposition hypotheses, in which the former dominates in soils with less microbial N limitation and the latter dominates in soils with relatively higher microbial N limitation. Our findings imply that N deposition may benefit soil carbon sequestration via suppressing PE, and highlight the need for field studies investigating the effects of nutrient addition on PE in the rhizosphere and in the subsoil.
TL;DR: Microbial life history traits can be used to link microbial community composition and metabolic processes with the turnover and transformation of SOC, and are suggested to be associated with several abundant microbial taxa.
Abstract: Microbial residues play a significant role in the formation of soil organic matter (SOM), but it is not clear how microbial traits influence residue accrual and SOM persistence. By pairing microbial biomarker and genomics approaches, we tested whether microbial life history strategies and residue accrual differed between primary (~70-year-old) and secondary (~30-year-old) subtropical forests. We found that microbial residue concentrations were significantly higher in secondary than primary forests, and strongly associated with several abundant microbial taxa (Ascomycota, Proteobacteria, Gemmatimonadetes). Microbial communities inhabiting resource-rich secondary forests were also associated with high growth yields and soil organic carbon (SOC) accrual (through residue retention), while nutrient-limited primary forests were dominated by microorganisms employing resource-acquisition strategies. We therefore suggest microbial life history traits can be used to link microbial community composition and metabolic processes with the turnover and transformation of SOC.
TL;DR: In this article, the authors investigate how long-term organic amendments change soil organic carbon mineralization via affecting the microbial community composition and their co-occurrence pattern from micro-to macroaggregates.
Abstract: Organic amendments can stimulate soil organic carbon (SOC) mineralization and soil aggregation simultaneously, which can improve C sequestration and soil fertility. However, the microbial mechanism governing C mineralization at the aggregate level remains uncertain. Here, we investigate how long-term organic amendments change SOC mineralization via affecting the microbial community composition and their co-occurrence pattern from micro-to macroaggregates. Four fertilization regimes from an 8-year field experiment were selected to study this mechanism, i.e., no fertilization (CK); inorganic NPK fertilizer (NPK); NPK + straw (NS); and NPK + straw and manure (NSM). Our results indicated that organic amendments significantly modified the C dynamics, bacterial and fungal community composition and network topological patterns in all aggregate sizes. Specifically, for microbial community composition, organic amendments increased the relative abundance of most Gram-negative bacteria and saprotrophic fungi. For microbial network relationships, organic amendments shifted keystone taxa from oligotrophs to copiotrophs in the bacterial network, and from Eurotiales to Sordariales in the fungal network, respectively. In addition, organic amendments alleviated competitive interactions coupled with keystone taxa in the bacterial network. These microbial changes were responsible for the increase of C mineralization in all aggregates, but the dominant microbial mechanisms varied with aggregate size. The alleviated competitive interactions coupled with keystone taxa of the bacterial network dominated the increases of C mineralization in macroaggregates, while the bacterial community composition did so in microaggregates. However, the fungal community composition only showed a significant impact on altering C mineralization in macroaggregates. Overall, our study provides a fundamental understanding of the microbial regulation of C dynamics at the aggregate level and highlights the importance of network topological patterns.
TL;DR: In this article, root exudates were simulated with 13C-labeled oxalic acid and 13Clabeled glucose to test whether indirect stimulation of microbial and extracellular enzyme activity leads to MAOM decomposition.
Abstract: Mineral-associated organic matter (MAOM) is considered a stable reservoir for soil nutrients that influences long-term soil carbon (C) and nitrogen (N) dynamics. However, recent experimental and theoretical evidence shows that root exudates may mobilize MAOM, thereby providing plants and microbes access to a large and N-rich pool. Given the mechanisms underlying MAOM C and N mobilization remain largely untested, we examined direct and indirect pathways by which root exudates destabilize this nutrient pool in laboratory mesocosms. We simulated root exudation with 13C-labeled oxalic acid to test whether root exudates are directly capable of mobilizing MAOM from mineral surfaces; and with 13C-labeled glucose to test whether indirect stimulation of microbial and extracellular enzyme activity leads to MAOM decomposition. We also tested the potential for oxalic acid and glucose to mobilize MAOM in an additional subset of sterilized soils to clarify the potential for non-microbial pathways of MAOM destabilization. Over the course of the 12-day MAOM incubation with and without simulated exudates, we measured C cycling (CO2 respiration rates, 13C–CO2 efflux), N cycling (inorganic N pools, gross N mineralization) and related microbial processes (enzyme activities and microbial community composition via phospholipid fatty acid analysis). Both of the simulated root exudates enhanced MAOM-C mineralization, with cumulative respiration increasing 35–89% relative to the water-only control. Likewise, glucose additions enhanced the production of an exo-cellulase and a chitinase by up to 130% and 39%, respectively, while oxalic acid enhanced oxidative enzyme activities up to 91% greater than control rates. We observed a positive association between glucose-induced shifts in enzyme activities, MAOM-C mineralization, and gross ammonification. Oxalic acid additions were associated with initial increases in fungal relative abundance and in sterile soils appeared to stimulate the release of metals and dissolved organic nitrogen into exchangeable pools. Our results indicate that common root exudates, like glucose and oxalic acid, can significantly increase the turnover and potential release of C and N from MAOM through indirect (e.g., enzyme induction) and direct (e.g., mobilization of metal oxides) mechanisms.
TL;DR: The soil microbiome was affected by both fertilizer and low pH in the 7th year of fertilization treatments, suggesting that the microbial community became more sensitive to environmental change under the influence of long-term excess N fertilizer.
Abstract: Nitrogen (N) fertilizer has often been generously applied to increase crop biomass yield. Although the influences of inorganic N fertilizer on soil microbial communities have been widely studied, the effect of N fertilizer on microbial co-occurrence networks and its metagenome is largely unknown. Further, seasonal changes in microbial community responses to N addition have rarely been reported. In this study, three N fertilizer rates (0, 56, 196 kg N/ha) were applied annually in switchgrass (Panicum virgatum L.) grown for bioenergy production in the upper Midwest, USA. The soil microbiome was affected by both fertilizer and low pH in the 7th year of fertilization treatments. The microbial community structures were relatively stable during the growing season for each N fertilizer rate. However, the excess N fertilizer (196N) increased the seasonal variation of bacterial and fungal communities. Network analysis showed that the microbial interactions at the 196N treatment were more intense, with decreased bacteria-fungal interactions compared to 56N and 0N. This suggests that the microbial community became more sensitive to environmental change under the influence of long-term excess N fertilizer. Metagenomic analysis showed that the long-term excess N fertilizer promoted many metabolic processes, especially carbohydrate and amino acid related metabolism and Archaea mediated ammonia oxidation. However, N fertilizer also reduced many other traits, especially N2 fixation and signal transduction, the latter of which may contribute to the decreased interactions between bacteria and fungi.
TL;DR: In this paper, a review describes how interactions between rotational and biological diversity drive biodiversity-function relationships, with positive impacts on the formation and storage of soil organic matter, including carbon allocation, rhizodeposition, and growth of rhizobiomes.
Abstract: Agricultural intensification has substantially reduced soil biodiversity as well as agroecosystem functions and services. Sustainable agroecosystems that increase crop diversity through rotation may promote soil biodiversity and above-belowground interactions. Studying ecological networks, soil communities, and abiotic impacts simultaneously increases our understanding of complex C cycling encompassing all components of a given system. Higher rotational diversity enhances primary productivity by increasing the photosynthetic intensity of crops in rotation relative to systems where a given crop is grown continuously. In addition, greater temporal crop diversity stimulates above-belowground interactions, which affects carbon allocation, rhizodeposition, and the growth of rhizobiomes. Stronger above-belowground interactions will intensify ecological connections between microbial and faunal networks among roots, rhizosphere, and bulk soil. This further strengthens soil functions and interactions between networks of biotic elements (plant inputs and soil food web functioning) and abiotic factors (soil matrix and microenvironments), providing positive feedback loops on soil organic C accrual. This review describes how interactions between rotational and biological diversity drive biodiversity-function relationships. By increasing the quantity, quality, and chemical diversity of C inputs, crop rotations with higher functional diversity foster soil communities and enhance biotic-abiotic interactions, with positive impacts on the formation and storage of soil organic matter.
TL;DR: In this article, the authors studied soil microbial CUE and NUE simultaneously using 18O-water tracer approach in a long-term N addition experiment in a temperate forest soil.
Abstract: Microbial elements use efficiencies are the important parameters in regulating soil carbon (C) and nitrogen (N) mineralization processes. Microbial C use efficiency (CUE) describes the proportion of C used for growth relative to the total organic C uptake. As such, high CUE values mean relatively less CO2 emission and more C retention in microbial biomass. Similarly, a higher microbial N use efficiency (NUE) indicates efficient biomass N sequestration and less N mineralization. However, very little is known how the microbial CUE and NUE are affected by N enrichment in forest soils. Here, we studied soil microbial CUE and NUE simultaneously using 18O-water tracer approach in a long-term N addition experiment comprising control (atmospheric N deposition, 2.7 g N m−2 yr−1), low N addition (atmospheric N deposition + 2.5 g N m−2 yr−1) and high N addition (atmospheric N deposition + 7.5 g N m−2 yr−1) in a temperate forest. We found microbial CUE responses to N addition were dependent on N addition rates and soil horizons. Specifically, low N addition significantly increased the microbial CUE by 45.12% while high N addition significantly reduced it by 27.84% in organic soil. Further, mineral soil microbial CUE did not change under low N addition but significantly increased by 133.18% under high N addition. We also found microbial NUE decreased with increasing N addition rate in organic soil but showed an opposite pattern in mineral soil. The stoichiometric imbalances associated with phosphorus between microbial biomass and resources and the microbial community changes under N addition were correlated with microbial CUE and NUE. Further, N addition decreased microbial biomass turnover in organic soil but accelerated it in mineral soil. Altogether, our results indicated that N addition could control soil C and N cycling processes by affecting microbial elements use efficiencies (i.e. CUE and NUE), which may consequently impact C and N sequestration in this temperate forest soil.
TL;DR: Novel evidence is provided that microbial communities in sorghum phyllosphere and root endosphere are more resistant than soil microbiota to long-term fertilization, and soil microbiota are important predictors of Sorghum yield and protein content.
Abstract: Crop harbors diverse microbial communities that profoundly influence host health and agricultural productivity. Crop habitat is a dynamic and heterogeneous environment, and thus crop microbiota may display spatial organization across different compartments. However, impacts of long-term fertilization, as a common agricultural practice, on the assembly of crop microbiota and their relationships with crop yield and quality remain largely unresolved. Here, we collected sorghum roots and leaves, and rhizosphere and bulk soils, from an eight-year field experiment with multiple fertilization regimes, and characterized sorghum-associated microbiomes by amplicon sequencing of bacterial 16S rRNA gene and fungal ITS region. Rhizosphere and bulk soils harbored significantly higher diversity of bacteria and fungi than phyllosphere and root endophytes, and the microbial community composition significantly differed across the four compartments. Fertilization significantly influenced the diversity and compositions of sorghum-associated microbial communities, but had more pronounced effects on rhizosphere and bulk soil microbiomes through altering the relative abundances of some major microbial biomarkers. Bacterial genera Lysobacter, Acidibacter, Steroidobacter, RB41, and Blastococcus, and fungal genera Fusarium and Guehomyces were the dominant microbial predictors of sorghum yield and protein content. Structural equation models revealed that fertilization had a positive and indirect effect on sorghum yield and protein content through influencing the microbial diversity in rhizosphere and bulk soils. We provide novel evidence that microbial communities in sorghum phyllosphere and root endosphere are more resistant than soil microbiota to long-term fertilization, and soil microbiota are important predictors of sorghum yield and protein content.
TL;DR: In this article, the authors define soil health as: "the vitality of a soil in sustaining the socio-ecological functions of its enfolding land" and propose that the point of pursuing the soil health metaphor is not merely to assign a number to the "goodness" of soil, but to generate understanding of relational mechanisms and thereby lead us to better nurture attributes that catalyze valued functions, now and perpetually.
Abstract: ‘Soil health’ has become a dominant, pervasive phrase in soil and environmental sciences. But despite its ubiquity, the concept remains elusively ambiguous, largely because ‘health’ here is a metaphor, not a literal scientific construct. So we ask: can this imagery nevertheless still advance research toward stewardship of soils globally? To address this question, we here define soil health as: ‘the vitality of a soil in sustaining the socio-ecological functions of its enfolding land.’ By this definition, soil health reflects not the composition of soil per se, rather its capacity to promote the pertinent functions of the land in which it is embedded. This means that the term has little meaning for a soil divorced from its ecosystem, and that properties conferring such health depend on place and time. From this view, we consider the metaphor's strengths and pitfalls for stewarding soils, and proffer some ways to elevate its use, mostly to spur conversation. We propose that the point of pursuing the soil health metaphor is not merely to assign a number to the ‘goodness’ of soil, but to generate understanding of relational mechanisms and thereby lead us to better nurture attributes that catalyze valued functions, now and perpetually. In the end, the continuing usefulness of the soil health metaphor depends, not on whether or not we can finally entrap it numerically, but whether it propels us to greater reverence for soil, deeper insight into its beneficial processes, and wiser ways of managing it. In time, when the health metaphor can no longer carry this prodigious weight, we may seek a worthy successor; a good metaphor produces good science, and good science produces ever better metaphors.
TL;DR: In this article, the relative influences of deterministic and stochastic processes in shaping microbial community assembly shift during secondary succession were investigated in soil microbial communities during long-term ecosystem recovery.
Abstract: Soil microbes re-establish plant diversity and ecosystem functions after disturbance events. Deterministic and stochastic processes are expected to contribute to microbial community assembly during long-term ecosystem recovery. We characterized soil prokaryotic and fungal communities, to determine their assembly patterns, along two chronosequences with early to later successional subtropical forests. Prokaryotic and fungal community composition was more variable in early successional forests but converged in the later successional forests. The community composition was governed by deterministic processes in the early stages, while the relative influence of stochasticity increased in the later stages. Environmental factors that predicted the shift in deterministic and stochastic balance varied within and across successional stages. In particular, the compositional dissimilarity of plant communities strongly predicted the relative influences of the two processes during succession. These findings suggest that the relative influences of deterministic and stochastic processes in shaping microbial community assembly shift during secondary succession. Consequently, plant communities are important predictors of assembly processes in soil microbial communities during long-term ecosystem recovery.
TL;DR: In this paper, the effects of 14C-labeled glucose addition to soil in the same final amounts (360μg−C g−1) split into two temporal patterns were evaluated.
Abstract: Labile carbon (C) inputs to soil (e.g., litter and root exudation) can prime soil organic matter (SOM) decomposition, and strongly influence SOM dynamics. The direction and intensity of priming, as well as the net C balance in soil, depend on the amount and frequency of labile C inputs. Most recent priming studies are based on single C additions, which are not truly representative of common litter inputs or root exudation in terrestrial ecosystems. Here, we evaluated the effects of 14C-labeled glucose addition to soil in the same final amounts (360 μg C g−1) split into two temporal patterns: seldom (20% of microbial biomass every two months) and frequent addition (4% of microbial biomass every 10 days) on the dynamics of CO2 production and SOM priming over a 200-day incubation. For the first time, we combined enzyme kinetics with substrate-induced growth respiration and fungal diversity to monitor microbially mediated SOM mineralization in response to the labile C input frequency. Frequent glucose addition decreased 14C incorporation into microbial biomass and almost doubled cumulative priming compared to seldom addition, resulting in a net loss of SOM for seldom and frequent C additions of −94 and −367 μg C g−1 respectively. Larger priming loss of SOM with frequent C inputs was accompanied by increased activities of β-glucosidase, chitinase, and acid phosphatase, and by a shift in fungal community towards increased abundance of K-strategist fungal species (mainly Mortierellales sp. and Trichoderma sp.) capable of SOM mineralization. In conclusion, frequent labile C inputs (e.g., rhizodeposits in rhizosphere or litterfall in disturephere) to soil will stimulate a shift in fungal community structure and functions, resulting in intensive priming of SOM decomposition and CO2 losses.
TL;DR: The stochastic and deterministic processes associated with the assembly of abundant and rare sub-communities of bacteria and fungi were quantified in different sized soil aggregates in apple orchards treated with a cover crop and fertilizer to facilitate a systematic approach to understand the mechanisms responsible for the changes in the fungal and bacterial community compositions.
Abstract: Soil bacterial and fungal communities often comprise the “abundant biosphere” and “rare biosphere”, which co-exist in soil aggregates to form a complex system of inter-species interactions. However, the different assembly processes exhibited by abundant and rare bacterial and fungal communities due to the spatial isolation of aggregates are still unclear. In this study, the stochastic and deterministic processes associated with the assembly of abundant and rare sub-communities of bacteria and fungi were quantified in different sized soil aggregates in apple orchards treated with a cover crop and fertilizer. The importance of variable selection in the assembly of the abundant bacterial community increased from macroaggregates to small microaggregates. The assembly of the rare bacterial community followed a transition from homogeneous selection to weak homogeneous selection with decreases in the soil organic carbon and total nitrogen contents. Both the abundant and rare bacterial community assemblies in soil aggregates were not limited in terms of their dispersal. The assembly of the abundant fungal community was dominated by stochastic processes, whereas the assembly of the rare fungal community was dominated by homogeneous selection and limited dispersal in different sized soil aggregates. The compositions of the abundant and rare bacterial and fungal communities were also affected by soil aggregates and agricultural practices. Most of the top 20 operational taxonomic units (OTUs) with high abundances among bacteria and fungi were related to the macroaggregate amounts compared with rare bacteria and fungi, and some OTUs among abundant fungi were related to the microaggregate and small microaggregate amounts. This study provides a priori hypotheses for testing in future experiments, thereby facilitating a systematic approach to understand the mechanisms responsible for the changes in the fungal and bacterial community compositions in different sized soil aggregates.
TL;DR: In this article, the dependence of microbial rates on temperature and moisture as well as their sensitivity when both variables change simultaneously has been investigated, and the authors found that microbial rates decreased with lower moisture and increased with higher temperatures until optimum values.
Abstract: It is of great importance to understand how terrestrial ecosystems will respond to global changes. However, most experimental approaches have focused on single factors. In natural systems, moisture and temperature often change simultaneously, and they can interact and shape microbial responses. Even though soil moisture and temperature are very important factors controlling microbial activity, there is disagreement on the dependence of microbial rates on temperature and moisture as well as their sensitivity when both variables change simultaneously. Here we created a moisture gradient and determined high resolution intrinsic temperature dependences for bacterial and fungal growth rates as well as respiration rates. We found that microbial rates decreased with lower moisture and increased with higher temperatures until optimum values. Additionally, we found independence between temperature and moisture as rate modifiers. We also found that temperature sensitivities (Q10) for microbial growth and respiration were not affected by changes in moisture. This provided an experimental framework to validate assumptions of temperature and moisture rate modifiers used in ecosystem and global cycling models (GCMs).
TL;DR: It was found that long-term N fertilization elevated the abundance of the microorganisms involved in most N-transforming processes but decreased that of N-fixing assemblages, suggesting the niche separation of these N-cycling taxa.
Abstract: Excessive nitrogen (N) fertilization in agricultural ecosystems strongly affects microbial N-cycling processes in soil. However, a comprehensive understanding of how microorganisms involved in each N transformation process respond to long-term N input is lacking. Here, using metagenomic sequencing combined with the direct assembly of N-cycling genes, we found that long-term N fertilization elevated the abundance of the microorganisms involved in most N-transforming processes but decreased that of N-fixing assemblages. The composition of the microbial groups involved in each N-transforming process was altered by fertilization, even though the abundance of several functional genes was not significantly changed. The relative abundance of microbial genera participating in the same step of N-cycling processes correlated with different soil properties, suggesting niche separation of these N-cycling taxa. Our results also indicated that the different responses to N fertilization exhibited by the taxa within the same functional group may be important for sustaining microbial nitrogen cycling in complex and dynamic environments.
TL;DR: In this article, the authors conducted a meta-analysis on the responses of soil carbon and P cycling and the stoichiometry of C, N and Ph cycling to the enhanced frequency and intensity of the freeze-thaw cycle (FTC) owing to global climate change.
Abstract: Enhanced frequency and intensity of freeze-thaw cycle (FTC) owing to global climate change may influence soil carbon (C) and phosphorus (P) cycling in terrestrial ecosystems. However, a comprehensive understanding of soil C and P cycling in response to FTC is still lacking. Here, we compiled data of 2471 observations from 75 publications and conducted a meta-analysis on the responses of soil C and P cycling and the stoichiometry of C, N and P cycling to FTC. Results showed that experimental FTC significantly increased soil dissolved organic C (+38%), instant and cumulative CH4 (+41% and +59%, respectively), dissolved organic C leaching (+62%), total salt-extractable P (+27%), dissolved organic P (+9.4%), leaching of dissolved total P (+312%), dissolved organic P (+30%), and dissolved inorganic P (+115%), and the ratio of available N to P (+21%). In contrast, soil microbial biomass C (−10%), cellulase activity (−16%), microbial biomass P (−10%), and the ratio of microbial biomass C to nitrogen (−8.1%) significantly decreased under FTC treatments. The likely reason for the increases in soluble soil C and P after FTC is the C and P release from dead soil microorganisms and changes in soil structure enhancing organic matter availability. The mean effect size of FTC generally increased with increasing FTC intensity, which was probably also the main reason for higher responses of soil C and P pools and fluxes to FTC observed in laboratory than in field experiments. However, mean effect sizes of FTC generally decreased with increasing duration and frequency of FTC, very likely due to substrate depletion through microbial uptake and leaching. The results of this meta-analysis contribute to a better understanding of the overall responses of soil C and P pools and fluxes to FTC, providing the basis for more accurate prediction of the impacts of future global climate change on biogeochemical cycles.
TL;DR: The authors explored the effect of soil texture on the fate of C from decomposing litter and the concurrent formation of soil organic matter (SOM) in mineral soils of different textures (sand-and clay-rich) and forest floor material.
Abstract: Incomplete knowledge on the environmental factors linking litter decomposition and the formation of soil organic matter (SOM) hampers the sustainable management of soil as a carbon (C) sink. Here, we explored the effect of soil texture on the fate of C from decomposing litter (Indiangrass; Sorghastrum nutans (L.) Nash) and the concurrent formation of SOM in mineral soils of different textures (sand- and clay-rich) and forest floor material. We quantified the amount of litter C respired, C remaining in the litter, and litter C retained in the soil/forest floor in a 186-day incubation employing stable isotope analyses (13C). We complemented our isotopic approach with the extraction of microbial biomarkers from the litter and soils/forest floor material and spectroscopic studies into the compositional changes of the incubated materials. We found that soil texture affected both the decomposition of litter and the retention of litter-derived C in the soil. The soil rich in clay provided conditions favorable for a more efficient microbial utilization of the litter material (high pH and high C use efficiency) as compared to the sand-rich soil and the forest floor. This resulted in lower amounts of litter C respired as CO2 (25.0%, vs. 55.6 and 56.1% in clay vs. sand and forest floor material, respectively) and higher amounts of litter C retained in the clay-rich soil (12.6% vs. 3.5 and 5.3% in clay vs. sand and forest floor material, respectively). High contents of silt- and clay-sized mineral particles in the clay-rich soil likely resulted in the ability to stabilize litter C in aggregates and organo-mineral associations, perhaps as microbial residues. This ability was low in the sand-rich soil and virtually absent in the forest floor, where the recalcitrance of the litter and native SOM was probably more relevant, and a larger portion of litter C may have been retained in the soil as relatively untransformed plant compounds. We emphasize that litter decomposition, the formation of SOM, and soil texture are tightly linked, such that any differences in soil texture alter litter decomposition and SOM formation patterns for the same litter.
TL;DR: In this paper, the first batch of regional-scale microbial necromass carbon (MNC) data based on amino sugars for the Qinghai-Tibet Plateau alpine grasslands was provided.
Abstract: Microbial necromass carbon (MNC) is key to soil organic carbon (SOC) storage. However, mechanisms regulating MNC accumulation on large scales are poorly understood. Here we provide the first batch of regional-scale MNC data based on amino sugars for the Qinghai-Tibet Plateau alpine grasslands. We show that Qinghai-Tibet grasslands have similar microbial biomass carbon (MBC) but lower MNC concentrations in SOC than Mongolian and other grasslands. The low contribution of MNC to SOC is mainly attributed to high aridity and low net primary productivity of the Qinghai-Tibet grasslands. Our findings highlight climatic and plant influences on MNC accumulation at regional scales.
TL;DR: A mechanism for P availability in subtropical successional forests based on AMF processes that increase the transformation of occluded P to labile and moderately labile Po forms, followed by acid phosphatase activity that converts these hydrolysable Po forms into inorganic P is proposed.
Abstract: Phosphorus (P) availability is a limiting factor for plant growth in tropical and subtropical regions, but many tropical and subtropical forests maintain high levels of productivity and biodiversity under P-limited conditions, which is why P limitation and plant community biomass increase simultaneously during succession in subtropical forests. Biologically-mediated P transformations in the rhizosphere are expected to increase P acquisition by plants during forest succession in tropical and subtropical regions. In this study, we collected leaf and rhizosphere samples from the dominant tree species in three successional forests (early, middle, and late) at the Dinghushan Biosphere Reserve, Southern China, and measured the leaf P concentrations and biological properties of the rhizosphere: microbial biomass P (MBP), P fractions, acid phosphatase activity, and the biomasses of arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF). We found that the leaf N:P ratio increased but the rhizosphere microbial biomass N:P ratio decreased from the early- to late-successional stages, indicating more plant P limitation and less microbial P limitation during forest succession. The decreased proportion of occluded P in the rhizosphere was negatively related to the increasing AMF biomass, and the increased proportions of labile organic P (Po) and moderately labile Po were positively associated with increasing AMF biomass but negatively related to the acid phosphatase activity that increased during forest succession. We propose a mechanism for P availability in subtropical successional forests based on AMF processes that increase the transformation of occluded P to labile and moderately labile Po forms, followed by acid phosphatase activity that converts these hydrolysable Po forms into inorganic P. Transformation of occluded P and Po fractions in the rhizosphere to plant-available P will satisfy the increasing P demand of plants during forest succession, thus maintaining the high productivity and biodiversity of P-limited tropical and subtropical forests.
TL;DR: A large-scale investigation in northern Australia found that the deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds, and Random forest model demonstrated that mean annual temperature was the most important predictor of both bacterial and fungal profiles in termites mounds.
Abstract: Termite mounds are an important habitat for an enormous diversity of microorganisms. However, the microbial community assembly processes in termite mounds remain unresolved, which impeded our ability to predict the biological functions of these mound-associated microbiota under the global changes. Here we conducted a large-scale investigation in northern Australia to explore biogeographical patterns of microbial community in termite mounds and identify the role of deterministic and stochastic processes in microbial community assembly. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungi had a stronger distance-decay relationship than bacteria. The neutral community model and normalized stochasticity ratio index (NST) revealed that the deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited a significantly weaker impact on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), likely due to the wider habitat niche breadth and higher potential migration rate of bacteria. Random forest model further demonstrated that mean annual temperature was the most important predictor of both bacterial and fungal profiles in termite mounds. These findings improved our understanding of spatial patterns and processes of microbiome in termite mounds, which is critical to decipher the role of termite mounds associated microbes in regulating ecosystem multifunctionality.
TL;DR: In this article, the authors assess how differences in the chemical composition of plant residues in combination with tillage management practices affect the local microbial community activity and structure, and subsequent soil aggregation and organic carbon and nitrogen dynamics in an organic, rainfed almond (Prunus dulcis Mill.) orchard.
Abstract: Soils play a major role in the global carbon cycle and are crucial to the management of climate change. Changes in plant cover derived from different agricultural practices induce variations in the quality of plant residue inputs and in the soil microbial community structure and activity, which may enhance the storage and protection of organic carbon (OC) and nitrogen (N) within aggregates. The aim of this study was to assess how differences in the chemical composition of plant residues in combination with tillage management practices affect the local microbial community activity and structure, and subsequent soil aggregation and OC and N dynamics in an organic, rainfed almond (Prunus dulcis Mill.) orchard. In the laboratory, three types of plant residue (shoots, roots, and the combination of both) coming from different species belonging to each agricultural practice (reduced tillage, reduced tillage plus green manure, reduced tillage plus organic manure, and no-tillage) were mixed with their respective soils and the CO2 released was measured over 243 days at 60% WHC and 28 °C. Water-stable aggregates (including microaggregates within macroaggregates), enzymatic activities related to carbon (dehydrogenase and β-glucosidase) and N (urease) cycling, and the microbial biomass and community structure through phospholipid fatty acid analysis, were measured at the end of the incubation period. Our results indicate that the chemical composition of plant residues controls the microbial community response, mediating decomposition and the incorporation of OC and N in stable aggregates. Therefore, the incorporation of labile and N-rich plant residues into the soil by reduced tillage is recommended since mixing roots and shoots from green manure increased the formation of free micro-aggregates and improved OC and N stabilization in our semiarid agroecosystem.