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1. Historical land use has long-term effects on microbial community assembly processes in forest soils

   https://doi.org/10.1038/s43705-021-00051-x  

   Osburn, Ernest D. ; Aylward, Frank O. ; Barrett, J. E. ( September 2021 , ISME Communications)

   Land use change has long-term effects on the structure of soil microbial communities, but the specific community assembly processes underlying these effects have not been identified. To investigate effects of historical land use on microbial community assembly, we sampled soils from several currently forested watersheds representing different historical land management regimes (e.g., undisturbed reference, logged, converted to agriculture). We characterized bacterial and fungal communities using amplicon sequencing and used a null model approach to quantify the relative importance of selection, dispersal, and drift processes on bacterial and fungal community assembly. We found that bacterial communities were structured by both selection and neutral (i.e., dispersal and drift) processes, while fungal communities were structured primarily by neutral processes. For both bacterial and fungal communities, selection was more important in historically disturbed soils compared with adjacent undisturbed sites, while dispersal processes were more important in undisturbed soils. Variation partitioning identified the drivers of selection to be changes in vegetation communities and soil properties (i.e., soil N availability) that occur following forest disturbance. Overall, this study casts new light on the effects of historical land use on soil microbial communities by identifying specific environmental factors that drive changes in community assembly.
2. The edaphic control of plant diversity

   https://doi.org/10.1111/geb.13151  

   Hulshof, Catherine M. ; Spasojevic, Marko J. ( July 2020 , Global Ecology and Biogeography)

   Abstract Background: The central thesis of plant ecology is that climate determines the global distribution of vegetation. Within a vegetation type, however, finer-scale environmental features, such as the physical and chemical properties of soil (edaphic variation), control patterns of plant diversity and distributions. Aims: Here, we review the literature to provide a mechanistic framework for the edaphic control of plant diversity. First, we review three examples where soils have known, prevalent effects on plant diversity: during soil formation, on unusual soils, and in regions with high edaphic heterogeneity. Second, we synthesize how edaphic factors mediate the relative importance of the four key processes of community assembly (speciation, ecological drift, dispersal, and niche selection). Third, we review the potential effects of climate change in edaphically heterogeneous regions. Finally, we outline key knowledge gaps for understanding the edaphic control of plant diversity. In our review, we emphasize floras of unusual edaphic areas (i.e., serpentine, limestone, granite), because these areas contribute disproportionately to the biodiversity hotspots of the world. Taxa: Terrestrial plants. Location: Global. Conclusion: Edaphic variation is a key driver of biodiversity patterns and influences the relative importance of speciation, dispersal, ecological drift, niche selection and interactions among these processes. Research ismore »still needed to gain a better understanding of the underlying mechanisms by which edaphic variation influences these community assembly processes and unusual soils provide excellent natural systems for such tests. Furthermore, the incorporation of edaphic variation into climate change research will help to increase the predictive power of species distribution models, identify potential climate refugia, and identify species with adaptations that buffer them from climate change. KEYWORDS: community assembly, edaphic, geodiversity, geology, gradient, heterogeneity, macroecology, soil« less
3. Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems

   https://doi.org/10.1128/mSystems.00098-20  

   Danczak, R. E. ; Daly, R. A. ; Borton, M. A. ; Stegen, J. C. ; Roux, S. ; Wrighton, K. C. ; Wilkins, M. J. ( April 2020 , mSystems)

   Lloyd, Karen G. (Ed.)

   ABSTRACT The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurfacemore »ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels. IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.« less
4. Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring

   https://doi.org/10.1128/AEM.01598-21  

   Fernandes-Martins, Maria C. ; Keller, Lisa M. ; Munro-Ehrlich, Mason ; Zimlich, Kathryn R. ; Mettler, Madelyn K. ; England, Alexis M. ; Clare, Rita ; Surya, Kevin ; Shock, Everett L. ; Colman, Daniel R. ; et al ( November 2021 , Applied and Environmental Microbiology)

   Semrau, Jeremy D. (Ed.)

   ABSTRACT Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating fastermore »growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.« less
5. Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils

   https://doi.org/10.1128/mBio.02521-18  

   Feng, Jiajie ; Penton, C. Ryan ; He, Zhili ; Van Nostrand, Joy D. ; Yuan, Mengting M. ; Wu, Liyou ; Wang, Cong ; Qin, Yujia ; Shi, Zhou J. ; Guo, Xue ; et al ( February 2019 , mBio)

   ABSTRACT Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N 2 fixation is the major source of biologically available N, the soil N 2 -fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene ( nifH ) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly ( P <  0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore,more »more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem. IMPORTANCE With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N 2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.« less