Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.

/pdf/keystone-taxa-as-drivers-of-microbiome-structure-and-3kqmhd75jv.pdf

Keystone taxa as drivers of microbiome structure and functioning

B6nassy, C., 1955. R6marques sur deux Aphelinid6s: Aphelinus mytilaspidis Le Baron et Aphytis proclia Walker. Annls l~piphyt. 6: 11-17. Lord, F. T. & MacPhee, A. W., 1953. The influence of spray programs on the fauna of apple orchards in Nova Scotia II. Oyster shell scale. Can. Ent. 79: 196-209. Pickett, A. D., 1946. A progress report on long term spray programs. Rep. Nova Scotia Fruit Grow. Ass. 83 : 27-31. Pickett, A. D., 1967. The influence of spray programs on the fauna of apple orchards in Nova Scotia XIV. Can. Ent. 97: 816-821. Tothill, J. D., 1918. The predacious mite Hemisarcoptes malus Shimer and its relation to the natural control of the oyster shell scale Lepidosaphes ulmi L. Agric. Gaz. Can. 5 : 234-239.

http://link.springer.com/content/pdf/10.1007/BF01976688.pdf

Soil enzymes: Kuprevich, V. F. & Shcherbakova, T. A.: Translated from the Russian edition (1966), published by the Indian National Scientific Documentation Centre, New Delhi 1971. 392 pp., offset printing from type script, paper cover. Obtainable from U.S. Department of Commerce, National Technical Information Service, Springfield, Va. 22151

Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.

/pdf/recent-understanding-of-soil-acidobacteria-and-their-1ei9779cwo.pdf

Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review.

Microbes play pivotal roles in soil organic matter (SOM) turnover: formation and decomposition. Organic fertilizers play crucial role for SOM accumulation, aggregate formation and influence microbial community composition and co-occurrence networks in microhabitats. Here, we investigated prokaryotic and fungal communities and their co-occurrence networks in four aggregate size classes in upland Ultisol following 27 years of mineral and/or organic fertilizer (rice straw, peanut straw, radish, or pig manure) application. Organic fertilizers and aggregate size classes have main and interactive effects on SOM content in aggregates (p  250 μm) than microaggregates (

Long-term manure application increases soil organic matter and aggregation, and alters microbial community structure and keystone taxa

Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes. Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system. Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.

/pdf/agricultural-management-and-plant-selection-interactively-37d456qj53.pdf

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

Fertilization has a large impact on the soil microbial communities, which play pivotal roles in soil biogeochemical cycling and ecological processes. While the effects of changes in nutrient availability due to fertilization on the soil microbial communities have received considerable attention, specific microbial taxa strongly influenced by long-term organic and inorganic fertilization, their potential effects and associations with soil nutrients remain unclear. Here we use deep 16S amplicon sequencing to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics (manure and straw)-inorganic fertilizers, and uncover potential links between soil nutrient parameters and specific bacterial taxa. Our results showed that combined organic-inorganic fertilization increased soil organic carbon (SOC) and total nitrogen (TN) contents and altered bacterial community composition, while inorganic fertilization had little impact on soil nutrients and bacterial community composition. SOC and TN emerged as the major determinants of community composition. The abundances of specific taxa, especially Arenimonas, Gemmatimonas and an unclassified member of Xanthomonadaceae, were substantially increased by organic-inorganic amendments rather than inorganic amendments only. A co-occurrence based network analysis demonstrated that SOC and TN had strong positive associations with some taxa (Gemmatimonas and the members of Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria and Bacteroidetes), and Gemmatimonas, Flavobacterium and an unclassified member of Verrucomicrobia were identified as the keystone taxa. These specific taxa identified above are implicated in the decomposition of complex organic matters and soil carbon, nitrogen and phosphorus transformations. The present work strengthens our current understanding of the soil microbial community structure and functions under long-term fertilization management and provides certain theoretical support for selection of rational fertilization strategies.

/pdf/bacterial-community-structure-after-long-term-organic-and-1t7a8hjf97.pdf

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations.

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Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations.