Coupling spatiotemporal community assembly processes to changes in microbial metabolism

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally-explicit multivariate statistics. We demonstrate that multiple selective pressures—imposed by sediment and porewater physicochemistry—integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally-stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

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Coupling spatiotemporal community assembly processes to changes in microbial metabolism

10.7287/peerj.preprints.2102v2 ◽

2016 ◽

Author(s):

Emily Graham ◽

Alex R. Crump ◽

Charles T Resch ◽

Sarah Fansler ◽

Evan Arntzen ◽

...

Keyword(s):

Conceptual Model ◽

Community Assembly ◽

Microbial Community Composition ◽

Microbial Metabolism ◽

Habitat Types ◽

Selective Pressures ◽

Ecological Selection ◽

Species Abundances ◽

Ecosystem Level ◽

Microbial Systems

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally-explicit multivariate statistics. We demonstrate that multiple selective pressures—imposed by sediment and porewater physicochemistry—integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally-stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

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Coupling spatiotemporal community assembly processes to ecosystem function

10.7287/peerj.preprints.2102v1 ◽

2016 ◽

Author(s):

Emily Graham ◽

Alex R. Crump ◽

Charles T Resch ◽

Sarah Fansler ◽

Evan Arntzen ◽

...

Keyword(s):

Ecosystem Function ◽

Community Assembly ◽

Seasonal Changes ◽

Model System ◽

Habitat Types ◽

Selective Pressures ◽

Species Abundances ◽

Compositional Changes ◽

And Function ◽

Response To Environmental Change

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types (e.g., attached and unattached) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally-explicit multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

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Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

10.21203/rs.3.rs-40339/v1 ◽

2020 ◽

Author(s):

xia ding ◽

Xiaojue Peng ◽

Zhichao Chen ◽

Yingjie Li ◽

Lihui Mao ◽

...

Keyword(s):

Microbial Community ◽

Drought Stress ◽

Microbial Communities ◽

Community Assembly ◽

Wild Rice ◽

Microbial Community Composition ◽

Α Diversity ◽

Oryza Longistaminata ◽

Network Properties ◽

Microbiome Assembly

Abstract Background Drought is a global environmental stress that limits crop yields. Microbial communities control many biogeochemical processes, and a predictive understanding of how crop microbial communities assemble in response to drought stress is central to addressing the challenges caused by drought. Little is known about the microbiome assembly processes in rice-ecosystems, particularly with regard to their environmental adaptation. Wild rice may serve as a source of superior drought tolerance candidate for rice breeding. There is an urgent need to explore wild rice resistance mechanisms to drought stress. Here, we evaluated the effect of drought stress on the microbial community recruitment and assembly in the endosphere (leaf, stem, and root) and rhizosphere of Oryza longistaminata. Results Species replacement was the dominant process shaping microbial community composition under drought stress. O. longistaminata recruited the phyla Actinobacteria and Fusobacteria, the genus Streptomyces, and phototrophic prokaryotes to improve its fitness. The host exerted strong effects on microbiome assembly, and the responses of the microbial community structure to the drought environment showed above- and belowground patterns. Drought reduced taxonomic α-diversity and destabilized co-occurrence network properties in the leaves and stems, but not in the roots and rhizosphere. Drought promoted the restructuring and strengthening of belowground network links to more strongly interconnect network properties. The drought response of the microbiome was phylogenetically conserved. Stochastic (neutral) processes acted on microbial community reassembly in response to drought stress across all four compartments. Conclusions Our results provide new insight into the mechanisms through which drought alters microbial community assembly in drought-tolerant wild rice and reveal a potential strategy for manipulating plant microbiomes to improve crop fitness.

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Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China

Forests ◽

10.3390/f11030285 ◽

2020 ◽

Vol 11 (3) ◽

pp. 285 ◽

Cited By ~ 1

Author(s):

Mengxin Zhao ◽

Jing Cong ◽

Jingmin Cheng ◽

Qi Qi ◽

Yuyu Sheng ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Community Assembly ◽

Soil Microbial Community ◽

Southern China ◽

Microbial Community Composition ◽

Nitrogen And Phosphorus ◽

Soil Microbial ◽

Microbial Community Assembly ◽

Microbial Functional Gene

Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.

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Searching for principles of microbial physiology

FEMS Microbiology Reviews ◽

10.1093/femsre/fuaa034 ◽

2020 ◽

Vol 44 (6) ◽

pp. 821-844

Author(s):

Frank J Bruggeman ◽

Robert Planqué ◽

Douwe Molenaar ◽

Bas Teusink

Keyword(s):

Experimental Data ◽

Growth Rate ◽

Evolutionary Biology ◽

Current Status ◽

Basic Principles ◽

Future Directions ◽

Selective Pressures ◽

State Growth ◽

Microbial Systems ◽

Working Out

ABSTRACT Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selective pressures and physicochemical constraints? If so, a broadly-applicable theory might be developed that predicts common microbiological behaviours. Microbial systems biologists have been working out the contours of this theory for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, metabolism, cell composition and steady-state growth. The theory makes predictions about fitness costs and benefits of protein expression, physicochemical constraints on cell growth and characteristics of optimal metabolisms that maximise growth rate. Comparisons of the theory with experimental data indicates that microorganisms often aim for maximisation of growth rate, also in the presence of stresses; they often express optimal metabolisms and metabolic proteins at optimal concentrations. This review explains the current status of the theory for microbiologists; its roots, predictions, experimental evidence and future directions.

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Species diversity and drivers of arbuscular mycorrhizal fungal communities in a semi-arid mountain in China

PeerJ ◽

10.7717/peerj.4155 ◽

2017 ◽

Vol 5 ◽

pp. e4155 ◽

Cited By ~ 16

Author(s):

He Zhao ◽

Xuanzhen Li ◽

Zhiming Zhang ◽

Yong Zhao ◽

Jiantao Yang ◽

...

Keyword(s):

Species Diversity ◽

Soil Texture ◽

Community Assembly ◽

Arable Land ◽

Arbuscular Mycorrhizal ◽

Forest Land ◽

Habitat Types ◽

Amf Diversity ◽

Amf Communities ◽

Semi Arid

Arbuscular mycorrhizal fungi (AMF) play an essential role in complex ecosystems. However, the species diversity and composition of AMF communities remain unclear in semi-arid mountains. Further, it is not well understood if the characteristics of AMF community assemblies differ for different habitat types, e.g., agricultural arable land, artificial forest land, natural grassland, and bush/wood land. Here, using the high-throughput technology by Illumina sequencing on the MiSeq platform, we explored the species diversity and composition of soil AMF communities among different habitat types in a semi-arid mountain (Taihang Mountain, Mid-western region of China). Then, we analyzed the effect of nutrient composition and soil texture on AMF community assembly. Our results showed that members of the Glomus genera were predominated in all soil types. The distance-based redundancy analysis indicated that the content of water, available phosphorus, and available potassium were the most crucial geochemical factors that significantly affected AMF communities (p < 0.05). The analysis of the soil texture confirmed that AMF diversity was negatively correlated with soil clay content. The comparison of AMF diversity among the various habitat types revealed that the artificial forest land had the lowest AMF diversity in comparison with other land types. Our findings suggest that there were differences in species diversity and composition of soil AMF communities among different habitat types. These findings shed new light on the characteristics of community structure and drivers of community assembly in AMF in semi-arid mountains, and point to the potential importance of different habitat types on AMF communities.

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Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

The ISME Journal ◽

10.1038/s41396-021-01111-9 ◽

2021 ◽

Author(s):

Ya-Jou Chen ◽

Pok Man Leung ◽

Perran L. M. Cook ◽

Wei Wen Wong ◽

Tess Hutchinson ◽

...

Keyword(s):

Microbial Community ◽

Community Assembly ◽

Microbial Community Composition ◽

Coastal Sediments ◽

Sediment Geochemistry ◽

Biogeochemical Processes ◽

Microbial Abundance ◽

Microbial Composition ◽

Hydrodynamic Disturbance ◽

Microbial Community Assembly

AbstractThe microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.

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Can functional traits explain phylogenetic signal in the composition of a plant community?

10.1101/032938 ◽

2015 ◽

Author(s):

Daijiang Li ◽

Anthoy R Ives ◽

Donald M Waller

Keyword(s):

Functional Traits ◽

Community Assembly ◽

Phylogenetic Signal ◽

Species Traits ◽

Functional Trait ◽

Phylogenetic Information ◽

Ecological Processes ◽

Forest Sites ◽

Species Abundances ◽

Understory Plant

Phylogeny-based and functional trait-based analyses are two principle ways to study community assembly and underlying ecological processes. In principle, knowing all information about species traits would make phylogenetic information redundant, at least that component of phylogenetic signal in the distribution of species among communities that is caused by phylogenetically related species sharing similar traits. In reality, phylogenies may contain more information than a set of singular, discretely measured traits because we cannot measure all species traits and may misjudge which are most important. The extent to which functional trait information makes phylogenetic information redundant, however, has not been explicitly studied with empirical data in community ecology. Here, we use phylogenetic linear mixed models to analyze community assembly of 55 understory plant species in 30 forest sites in central Wisconsin. These communities show strong phylogenetic attraction, yet variation among sites in 20 environmental variables could not account for this pattern. Most of the 15 functional traits we measured had strong phylogenetic signal, but only three varied strongly among sites in ways that affected species' abundances. These three traits explained only 19% of variation in phylogenetic patterns of species co-occurrence. Thus, phylogenies appear to provide considerably more information about community assembly than the functional traits measured in this study, demonstrating the value of phylogeny in studying of community assembly processes even with abundant functional traits.

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Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz058 ◽

2019 ◽

Vol 95 (6) ◽

Cited By ~ 1

Author(s):

Anders Bjørnsgaard Aas ◽

Carrie J Andrew ◽

Rakel Blaalid ◽

Unni Vik ◽

Håvard Kauserud ◽

...

Keyword(s):

Microbial Community ◽

Spatial Structure ◽

Community Assembly ◽

High Throughput Sequencing ◽

Spatial Scales ◽

Microbial Community Composition ◽

Diversity Patterns ◽

Bistorta Vivipara ◽

Adjacent Soil ◽

Bacteria And Fungi

ABSTRACT The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.

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