To link microbial community 16S structure to a measured function in a natural soil, we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial ...community. β-Glucosidase activity was assayed in 450 individual aggregates, which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be observed that functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to the presence or absence of particular taxonomic groups.
Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although ...microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg(2+) and SO(2-) 4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.
Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. ...However, the ecological mechanisms regulating long‐term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade‐long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance >1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%–82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche‐based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas.
The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given ...that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.
Aim: A long-standing challenge in ecology is to identify the suite of factors that lead to turnover in species composition in both space and time. These factors might be stochastic (e.g. sampling and ...priority effects) or deterministic (e.g. competition and environmental filtering). While numerous studies have examined the relationship between turnover and individual drivers of interest (e.g. primary productivity, habitat heterogeneity, or regional –'gamma' – diversity), few studies have disentangled the simultaneous influences of multiple stochastic and deterministic processes on both temporal and spatial turnover. If turnover is governed primarily by stochastic sampling processes, removing the sampling effects of gamma diversity should result in non-significant relationships between turnover and environmental variables. Conversely, if deterministic processes govern turnover patterns, removing sampling effects will have little influence on turnover gradients. Here, we test these predictions. Location: The United States. Methods: Continental-scale, multidecadal data were used to quantify spatial and temporal turnover in avian community composition within 295 survey routes. A series of regression and structural equation models were coupled with a null model to construct statistical models describing turnover patterns. Results: Examining explanatory variables alone or in combination showed that spatial and temporal turnover increased together, decreased with primary productivity and increased with habitat heterogeneity. The relationships between turnover and all variables became weaker when sampling effects were removed, but relationships with primary productivity and habitat heterogeneity remained relatively strong. In addition, spatial turnover increased strongly with spatial gamma diversity after sampling effects were removed. Main conclusions: Our results show that spatial and temporal turnover are related to each other through a stochastic sampling process, but that each type of turnover is further influenced by deterministic processes. The relative influence of deterministic processes appears, however, to decrease with primary productivity and increase with habitat heterogeneity across an east-west longitudinal gradient in North America.
Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw. We hypothesize that permafrost ...communities are shaped by physical constraints imposed by prolonged freezing, and exhibit spatial distributions that reflect dispersal limitation and selective pressures associated with these physical constraints. To test this, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16) and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2 = 0.14, P = 0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings suggest that the dominant processes shaping microbial communities in permafrost result from the stability of the permafrost environment, which imposes dispersal and thermodynamic constraints.
Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer ...have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTI
), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTI
, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTI
can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTI
values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family
were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTI
offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.
A component of metabolic scaling theory has worked towards understanding the influence of metabolism over the generation and maintenance of biodiversity. Specific models within this 'metabolic theory ...of biodiversity' (MTB) have addressed temperature gradients in speciation rate and species richness, but the scope of MTB has been questioned because of empirical departures from model predictions. In this study, we first show that a generalized MTB is not inconsistent with empirical patterns and subsequently implement an eco-evolutionary MTB which has thus far only been discussed qualitatively. More specifically, we combine a functional trait (body mass) approach and an environmental gradient (temperature) with a dynamic eco-evolutionary model that builds on the current MTB. Our approach uniquely accounts for feedbacks between ecological interactions (size-dependent competition and predation) and evolutionary rates (speciation and extinction). We investigate a simple example in which temperature influences mutation rate, and show that this single effect leads to dynamic temperature gradients in macroevolutionary rates and community structure. Early in community evolution, temperature strongly influences speciation and both speciation and extinction strongly influence species richness. Through time, niche structure evolves, speciation and extinction rates fall, and species richness becomes increasingly independent of temperature. However, significant temperature-richness gradients may persist within emergent functional (trophic) groups, especially when niche breadths are wide. Thus, there is a strong signal of both history and ecological interactions on patterns of species richness across temperature gradients. More generally, the successful implementation of an eco-evolutionary MTB opens the perspective that a process-based MTB can continue to emerge through further development of metabolic models that are explicit in terms of functional traits and environmental gradients.
River corridors are fundamental components of the Earth system, and their biogeochemistry can be heavily influenced by processes in subsurface zones immediately below the riverbed, referred to as the ...hyporheic zone. Within the hyporheic zone, organic matter (OM) fuels microbial respiration, and OM chemistry heavily influences aerobic and anaerobic biogeochemical processes. The link between OM chemistry and respiration has been hypothesized to be mediated by OM molecular diversity, whereby respiration is predicted to decrease with increasing diversity. Here we test the specific prediction that aerobic respiration rates will decrease with increases in the number of unique organic molecules (i.e., OM molecular richness, as a measure of diversity). We use publicly available data across the United States from crowdsourced samples taken by the Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (WHONDRS) consortium. Our continental-scale analyses rejected the hypothesis of a direct limitation of respiration by OM molecular richness. In turn, we found that organic carbon (OC) concentration imposes a primary constraint over hyporheic zone respiration, with additional potential influences of OM richness. We specifically observed respiration rates to decrease nonlinearly with the ratio of OM richness to OC concentration. This relationship took the form of a constraint space with respiration rates in most systems falling below the constraint boundary. A similar, but slightly weaker, constraint boundary was observed when relating respiration rate to the inverse of OC concentration. These results indicate that maximum respiration rates may be governed primarily by OC concentration, with secondary influences from OM richness. Our results also show that other variables often suppress respiration rates below the maximum associated with the richness-to-concentration ratio. An important focus of future research will identify physical (e.g., sediment grain size), chemical (e.g., nutrient concentrations), and/or biological (e.g., microbial biomass) factors that suppress hyporheic zone respiration below the constraint boundaries observed here.
Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits ...on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (
colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to "cross-feeding" with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during
colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition.
The influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were "cross-fed" with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.
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