Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews, Год журнала: 2017, Номер 81(4)

Опубликована: Окт. 12, 2017

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly microbial ecology. Although stochastic processes are believed to play nonnegligible roles shaping structure, their importance relative deterministic hotly debated. The of ecological stochasticity structure far less appreciated. Some main reasons for such heavy debates difficulty defining diverse methods used delineating stochasticity. Here, we provide critical review synthesis data from most recent studies on assembly We then describe both components embedded various processes, including selection, dispersal, diversification, drift. also different approaches inferring observational diversity patterns highlight experimental communities. In addition, research challenges, gaps, future directions research.

Язык: Английский

---

Function and functional redundancy in microbial systems

Nature Ecology & Evolution, Год журнала: 2018, Номер 2(6), С. 936 - 943

Опубликована: Апрель 12, 2018

Язык: Английский

---

Emergent simplicity in microbial community assembly

Science, Год журнала: 2018, Номер 361(6401), С. 469 - 474

Опубликована: Авг. 3, 2018

Interchanging species of similar function Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range contexts, from biotechnological applications to what happens our guts. Goldford et al. sampled the microbial soil plants containing hundreds thousands sequence variants. The organisms were passaged after culture low concentrations single carbon sources cross-fed with each other's metabolites; then, resulting sequenced using 16S ribosomal RNA, outcomes modeled mathematically. mix that survived under steady conditions converged reproducibly reflect experimentally imposed rather than initially inoculated—although at coarse phylogenetic levels, taxonomic patterns persisted. Science , this issue p. 469

Язык: Английский

---

The evolution of the host microbiome as an ecosystem on a leash

Nature, Год журнала: 2017, Номер 548(7665), С. 43 - 51

Опубликована: Авг. 1, 2017

Язык: Английский

---

Research priorities for harnessing plant microbiomes in sustainable agriculture

PLoS Biology, Год журнала: 2017, Номер 15(3), С. e2001793 - e2001793

Опубликована: Март 28, 2017

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is integrate beneficial plant microbiomes—i.e., those enhancing growth, nutrient use efficiency, abiotic stress tolerance, disease resistance—into agricultural This integration will require large-scale effort among academic researchers, industry farmers understand manage plant-microbiome interactions context modern systems. Here, we identify priorities for research this area: (1) develop model host–microbiome systems crop plants non-crop with associated microbial culture collections reference genomes, (2) define core microbiomes metagenomes systems, (3) elucidate rules synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms interactions, (5) characterize refine genotype-by-environment-by-microbiome-by-management interactions. Meeting should accelerate our ability design implement effective manipulations management strategies, which, turn, pay dividends both consumers producers supply.

Язык: Английский

---

Let the Core Microbiota Be Functional

Trends in Plant Science, Год журнала: 2017, Номер 22(7), С. 583 - 595

Опубликована: Май 23, 2017

Язык: Английский

---

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Nature Genetics, Год журнала: 2022, Номер 54(2), С. 134 - 142

Опубликована: Фев. 1, 2022

Язык: Английский

---

Trophic Interactions and the Drivers of Microbial Community Assembly

Current Biology, Год журнала: 2020, Номер 30(19), С. R1176 - R1188

Опубликована: Окт. 1, 2020

Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found animal guts, oceans, or soils, it is still unclear whether there are generalizable biological ecological processes that control their dynamics function. Here, we review experimental theoretical advances to argue networks trophic interactions, which the metabolic excretions one primary resource for another, constitute central drivers community assembly. Trophic interactions emerge from deconstruction complex forms organic matter into a wealth smaller intermediates, some released environment serve nutritional buffet community. The structure emergent network rate at resources supplied many features assembly, including relative contributions competition cooperation emergence alternative states. Viewing assembly through lens also has important implications spatial communities well functional redundancy taxonomic groups. Given ubiquity across environments, they impart common logic can enable development more quantitative predictive ecology.

Язык: Английский

---

Deciphering functional redundancy in the human microbiome

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Дек. 4, 2020

Abstract Although the taxonomic composition of human microbiome varies tremendously across individuals, its gene or functional capacity is highly conserved — implying an ecological property known as redundancy. Such redundancy has been hypothesized to underlie stability and resilience microbiome, but this hypothesis never quantitatively tested. The origin still elusive. Here, we investigate basis for in by analyzing genomic content network a bipartite graph that links microbes genes their genomes. We find exhibits several topological features favor high Furthermore, develop simple genome evolution model generate network, finding moderate selection pressure horizontal transfer rate are necessary networks with key Finally, analyze data from two published studies fecal microbiota transplantation (FMT), recipient’s pre-FMT raises barriers donor engraftment. This work elucidates potential evolutionary processes create maintain contribute resilience.

Язык: Английский

---

Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 2937 - 2958

Опубликована: Май 16, 2020

Abstract A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on biodiversity and functioning ecosystems is yet to be implemented by regulatory frameworks. Despite broadly acknowledged potential genomics this end, technical limitations conceptual issues still stand way its broad application end‐users. In addition, multiplicity implementation strategies may contribute a perception that routine methodology premature or “in development”, hence restraining regulators from binding these tools into legal Here, we review recent implementations methods, applied biomonitoring ecosystems. By taking general overview, without narrowing our perspective particular habitats groups organisms, paper aims compare, discuss strengths four for monitoring: (a) Taxonomy‐based analyses focused identification known bioindicators described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; (d) Functional (metagenomics metatranscriptomics). We emphasise utility three latter integrate meiofauna microorganisms are not traditionally utilised because difficult taxonomic identification. Finally, propose roadmap programmes leverage analytical advancements, while pointing out current future research needs.

Язык: Английский

---