Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community ...assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.
Discerning network interactions among different species/populations in microbial communities has evoked substantial interests in recent years, but little information is available about temporal ...dynamics of microbial network interactions in response to environmental perturbations. Here, we modified the random matrix theory‐based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time‐series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. Particularly, several keystone sulfate‐reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.
lPhylogenetic group based AS assembly is identified by long time data of two WWTPs.lThe assembly of one third (relative abundance) AS community is deterministic-dominated.lThe microbial diversity ...pattern is more stable in AS than influent community.lThe composition of AS community has a seasonal succession pattern.lThe network structure of AS community is more stable in summer and autumn.
The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using “Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)”. The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.
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Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a ...microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data.
Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA).
The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Recent studies have demonstrated the ability for polystyrene (PS) degradation within the gut of mealworms (Tenebrio molitor). To determine whether plastics may be broadly susceptible to ...biodegradation within mealworms, we evaluated the fate of polyethylene (PE) and mixtures (PE + PS). We find that PE biodegrades at comparable rates to PS. Mass balances indicate conversion of up 49.0 ± 1.4% of the ingested PE into a putative gas fraction (CO2). The molecular weights (M n) of egested polymer residues decreased by 40.1 ± 8.5% in PE-fed mealworms and by 12.8 ± 3.1% in PS-fed mealworms. NMR and FTIR analyses revealed chemical modifications consistent with degradation and partial oxidation of the polymer. Mixtures likewise degraded. Our results are consistent with a nonspecific degradation mechanism. Analysis of the gut microbiome by next-generation sequencing revealed two OTUs (Citrobacter sp. and Kosakonia sp.) strongly associated with both PE and PS as well as OTUs unique to each plastic. Our results suggest that adaptability of the mealworm gut microbiome enables degradation of chemically dissimilar plastics.
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.
•Microbial functional diversity positively regulates soil multifunctionality.•Microbial diversity contributes more to multifunctionality than taxonomic traits.•Soil aggregate size may indirectly and negatively determine multifunctionality.•Organic and inorganic fertilizers have opposite effects on multifunctionality.•Soil nutrition and functional diversity together control multifunctionality.
Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less ...studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.
Summary
Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the ...stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change and sampled the soils annually after harvesting the maize over the following 6 years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. A continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling genes were detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities.
Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species ...abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a "hunger games" hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.
As the second-largest terrestrial carbon (C) flux, soil respiration (R
) has been stimulated by climate warming. However, the magnitude and dynamics of such stimulations of soil respiration are ...highly uncertain at the global scale, undermining our confidence in future climate projections. Here, we present an analysis of global R
observations from 1987-2016. R
increased (P < 0.001) at a rate of 27.66 g C m
yr
(equivalent to 0.161 Pg C yr
) in 1987-1999 globally but became unchanged in 2000-2016, which were related to complex temporal variations of temperature anomalies and soil C stocks. However, global heterotrophic respiration (R
) derived from microbial decomposition of soil C increased in 1987-2016 (P < 0.001), suggesting accumulated soil C losses. Given the warmest years on records after 2015, our modeling analysis shows a possible resuscitation of global R
rise. This study of naturally occurring shifts in R
over recent decades has provided invaluable insights for designing more effective policies addressing future climate challenges.
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