Significant differences in the microbial biomass and diversity in soil have been observed following long-term fertilization, but little research has explored the co-occurrence patterns among microbial taxa or functions. Soil samples from four long-term experiments in China were collected, and an Illumina amplicon sequencing of 16S rDNA amplicon was performed to decipher the differences in interactions and network organization arising from fertilization with organic amendment (OA) or chemical fertilizer (CF) across the sampling sites. We thus aimed to extend the analysis beyond the basic inventory descriptions of the composition and diversity of the microbiome and toward an assessment of relationships and effects. Nonmetric multidimensional scaling analysis revealed a clear difference between the soil microbiomes associated with the OA and CF treatments. Fertilization can interact with the soil chemical properties and sampling site, thereby significantly impacting the associated soil microbiome. Distinct network structures indicated that the OA network was characterized by more functionally interrelated operational taxonomic units (OTUs) than the CF network. The topological roles of individual OTUs and key microbial populations were distinctly different, although the generalists mainly belonging to Actinobacteria and Proteobacteria were observed in both networks. The different fertilization treatments had distinct effects on the soil pH, which represented a key variable to impact the associated microbial community modularity. Most functional groups involving carbon-, nitrogen- and phosphorus-related metabolism and recycling and antibiotic biosynthesis were present at significantly high abundance in the organic-amended soils. All of the functions with statistical significance could be traced to corresponding responsible major modules in the CF network, but it was not the case in OA soil. These results suggested that the soil functions were decentralized and assigned to small groups in OA soil. Overall, we demonstrated that long-term organic amendment supports stronger functional potentials and more interactions within soil community relative to long-term chemical-only fertilization, which may be related to OA benefits to soil stability and buffering capacity. These results explore the correlations, inter-taxa and between major groups and functional traits, to gain a more integrated understanding of microbiome and ecological rules guiding soil community fostered by fertilization regimes.

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis

Soil carbon (C) stabilisation is known to depend in part on its distribution in structural aggregates, and upon soil microbial activity within the aggregates. However, the mechanisms and relative contributions of different microbial groups to C turnover in different aggregates under various management practices remain unclear. The aim of this study was to determine the role of soil aggregation and their associated microbial communities in driving the responses of soil organic matter (SOM) to multiple management practices. Our results demonstrate that higher amounts of C inputs coupled with greater soil aggregation in residue retention management practices has positive effects on soil C content. Our results provide evidence that different aggregate size classes support distinct microbial habitats which supports the colonisation of different microbial communities. Most importantly our results indicate that the effects of management practices on soil C is modulated by soil aggregate sizes and their associated microbial community and are more pronounced in macro-aggregate compared with micro-aggregate sizes. Based on our findings we recommend that differential response of management practices and microbial control on the C turnover in macro-aggregates and micro-aggregate should be explicitly considered when accounting for management impacts on soil C turnover.

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content.

Alkaline phosphomonoesterase (ALP) mainly originates from soil microbial secretion and plays a crucial role in the turnover of soil phosphorus (P). To examine the response of ALP-encoding microbial communities (analysed for the biomarker of the ALP gene, phoD) of soils and derivative soil fractions to different fertilisation regimes, soil samples were collected from a long-term experimental field (over 35 years). The different organic P (Po) pools of soil fractions and the ALP activity of soil were also determined. Compared with chemical-only fertilised soils, the ALP activity was 232–815% higher in organic-amended soils, and the highest enzyme activity was observed in the organic-only fertilised treatment. The abundance of the phoD gene harbouring in soil fractions, determined by quantitative PCR (qPCR), was affected by different fertilisations. The highest abundance of the phoD gene was generally detected in the 2–63-μm-sized fraction (silt), but most phoD-encoding microbial species were associated to the 0.1–2-μm-sized fraction (clay) in the chemical-only fertilised soil. The contents of labile Po (LPo), moderately labile Po (MLPo) and fulvic acid-associated Po (FAPo) were significantly correlated with the phoD gene abundance, whereas only LPo content was significantly correlated with the ALP activity. The dominant phoD-encoding phylas were Actinobacteria and Proteobacteria, according to a high-throughput sequencing. Bradyrhizobium, a N2-fixer identified as a phoD-encoding genus, showed the highest abundance in fertilised soils. The abundance of Bradyrhizobium, Streptomyces, Modestobacter, Lysobacter, Frankia and Burkholderia increased with the organic-only amendment and was significantly correlated with the ALP activity. According to structure equation models (SEM), pH and LPo content significantly and directly affected the ALP activity; the soil organic C (Corg) content was related to composition and abundances of phoD-harbouring microbial communities; since both microbial properties were correlated to the ALP activity, the Corg content was indirectly related to the ALP activity. In conclusion, soil management practices can be used to optimise the contents of soil available P and the organic P with regulation of soil ALP activity and the community composition of corresponding microbes.

Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions

Understanding the influence of long-term crop management practices on the soil microbial community is critical for linking soil microbial flora with ecosystem processes such as those involved in soil carbon cycling. In this study, pyrosequencing and a functional gene array (GeoChip 4.0) were used to investigate the shifts in microbial composition and functional gene structure in a medium clay soil subjected to various cropping regimes. Pyrosequencing analysis showed that the community structure (β-diversity) for bacteria and fungi was significantly impacted among different cropping treatments. Functional gene array-based analysis revealed that crop rotation practices changed the structure and abundance of genes involved in C degradation. Significant correlations were observed between the activities of four enzymes involved in soil C degradation and the abundance of genes responsible for the production of respective enzymes, suggesting that a shift in the microbial community may influence soil C dynamics. We further integrated physical, chemical, and molecular techniques (qPCR) to assess relationships between soil C, microbial derived enzymes and soil bacterial community structure at the soil micro-environmental scale (e.g. within different aggregate-size fractions). We observed a dominance of different bacterial phyla within soil microenvironments which was correlated with the amount of C in the soil aggregates suggesting that each aggregate represents a different ecological niche for microbial colonization. Significant effects of aggregate size were found for the activity of enzymes involved in C degradation suggesting that aggregate size distribution influenced C availability. The influence of cropping regimes on microbial and soil C responses declined with decreasing size of soil aggregates and especially with silt and clay micro-aggregates. Our results suggest that long term crop management practices influence the structural and functional potential of soil microbial communities and the impact of crop rotations on soil C turnover varies between different sized soil aggregates. These findings provide a strong framework to determine the impact of management practices on soil C and soil health.

/pdf/soil-aggregate-size-mediates-the-impacts-of-cropping-regimes-2hh72w6cr4.pdf

Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities

Response of soil physicochemical properties and enzyme activities to long-term reclamation of coastal saline soil, Eastern China

Particle-size soils were fractionated for evaluating changes in the composition of bacterial community and enzyme activity in response to 13 years of fertilization. This study focused on Mollisol and its particle-size fractions of 200–2,000 μm (coarse sand sized), 63 to 200 μm (fine sand sized), 2 to 63 μm (silt sized), and 0.1 to 2 to μm (clay-sized). Long-term chemical fertilization lowered the pH of all particle fractions, whereas organic fertilizer application mitigated soil acidification. Nutrient concentrations depended on both fertilizer treatment and particle fractions and enzymes were unevenly active throughout the soil. Generally, the highest enzyme activities were observed in the silt and clay fractions of control soil and the soil treated with chemical fertilizer (N, P, and K (NPK)) and in the sand-sized fraction of soil treated with manure and chemical fertilizer (MNPK). Except for acid phosphomonoesterase, the other tested enzyme activities in coarse-sized fractions of MNPK soil were significantly higher than those of the control and NPK soils. Fertilization and soil fraction interactively (p < 0.05) affected the enzyme activity. Denaturing gradient gel electrophoresis analysis showed that the bacterial community structure significantly differed in different particle sizes with a higher bacterial diversity in small-sized than in coarse-sized fractions. Dominant bands were excised and sequenced. We have found the following bacterial groups: Actinobacteria, γ-proteobacteria, and Acidobacteria. In addition, enrichment of organic matter in coarser fractions was related to greater bacterial diversity than any other treatment. Principal component analysis showed a smaller variability among fractions of the organic amended treatment. Redundancy analysis showed that the tested properties significantly affected the composition of bacterial community with the exception of C/N and available P. No significant correlation between enzyme activity and bacterial community composition was detected, whereas positive correlations between other soil properties and enzyme activities were observed to various extents. Probably, enzyme activities might be affected by specific functional bacterial communities rather than by the overall bacterial community. We concluded that the long-term application of organic manures contributed to the increase of soil organic matter content of particles higher than 200 mm, with higher bacterial diversity and increases in most of the enzyme activities.

Response of the bacterial diversity and soil enzyme activity in particle-size fractions of Mollisol after different fertilization in a long-term experiment

Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.

/pdf/quantitative-and-compositional-responses-of-ammonia-1jjfe66iul.pdf

Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization.

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Response of the bacterial diversity and soil enzyme activity in particle-size fractions of Mollisol after different fertilization in a long-term experiment

Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization.