Does diversity beget diversity in microbiomes? DOI Creative Commons
Naïma Madi, Michiel Vos, Carmen Lía Murall

et al.

eLife, Journal Year: 2020, Volume and Issue: 9

Published: Nov. 20, 2020

Microbes are embedded in complex communities where they engage a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested explain how species could influence diversity. 'Ecological Controls' (EC) predicts negative relationship, the evolution migration novel types constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) positive with existing promoting accumulation further via niche construction other Using high-throughput amplicon sequencing data from Earth Microbiome Project, we provide evidence that DBD strongest low-diversity biomes, but weaker more diverse consistent biotic initially favouring (as predicted by DBD). However, increasingly filled, hits plateau EC).

Language: Английский

Microbial diversity in extreme environments DOI

Wensheng Shu,

Li‐Nan Huang

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(4), P. 219 - 235

Published: Nov. 9, 2021

Language: Английский

Citations

364
Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide DOI Creative Commons
Zahra F. Islam, Paul R. F. Cordero,

Joanna Feng

et al.

The ISME Journal, Journal Year: 2019, Volume and Issue: 13(7), P. 1801 - 1813

Published: March 14, 2019

Abstract Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. this study, we investigated the sources that support persistence of two thermophilic strains environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved molecular hydrogen (H2), carbon monoxide (CO), sulfur compound oxidation significantly upregulated. Gas chromatography microsensor experiments showed T. aerobically respires H2 CO at a range relevant concentrations sub-atmospheric levels. Phylogenetic analysis suggests hydrogenases mediating processes are widely distributed Chloroflexi genomes have probably been horizontally acquired on more than one occasion. Consistently, confirmed sporulating isolate Thermogemmatispora sp. T81 Ktedonobacteria) also oxidises atmospheric during persistence, though further studies required determine if findings extend mesophilic strains. This provides axenic culture evidence supports bacterial reports third phylum, following Actinobacteria Acidobacteria, be experimentally shown mediate biogeochemically ecologically important process oxidation. adds growing body trace gases dependable for persistence.

Language: Английский

Citations

149
Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs DOI
Qing He, Shang Wang, Weiguo Hou

et al.

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 772, P. 145465 - 145465

Published: Jan. 30, 2021

Language: Английский

Citations

125
Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons DOI Creative Commons
Gabriela Kapinusová, Marco A. Lopez Marin, Ondřej Uhlík

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: March 7, 2023

In terms of the number and diversity living units, prokaryotic empire is most represented form life on Earth, yet it still to a significant degree shrouded in darkness. This microbial “dark matter” hides great deal potential phylogenetically or metabolically diverse microorganisms, thus important acquire them pure culture. However, do we know what microorganisms really need for their growth, obstacles are cultivation previously unidentified taxa? Here review common sometimes unexpected requirements environmental especially soil-harbored bacteria, needed replication cultivation. These include resuscitation stimuli, physical chemical factors aiding cultivation, growth factors, co-cultivation laboratory natural neighborhood.

Language: Английский

Citations

45
Island biogeography of soil bacteria and fungi: similar patterns, but different mechanisms DOI Creative Commons
Shaopeng Li, Pandeng Wang, Yongjian Chen

et al.

The ISME Journal, Journal Year: 2020, Volume and Issue: 14(7), P. 1886 - 1896

Published: April 27, 2020

Abstract Microbes, similar to plants and animals, exhibit biogeographic patterns. However, in contrast with the considerable knowledge on island biogeography of higher organisms, we know little about distribution microorganisms within among islands. Here, explored insular soil bacterial fungal underlying mechanisms, using microbiota from a group land-bridge islands as model system. Similar species-area relationships observed for many macroorganisms, both island-scale diversity increased area; neither diversity, however, was affected by isolation. By contrast, communities exhibited strikingly different assembly patterns The loss smaller driven primarily systematic decline samples, whereas homogenization community composition samples. Lower moisture limited within-sample spatial distances samples restricted among-sample These results indicate that among-island differences habitat quality generate relationship, within-island dispersal limitation generates relationship. Together, our study suggests mechanisms underlie bacteria fungi.

Language: Английский

Citations

126
Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland DOI Creative Commons
Peter T. Podar,

Zamin K. Yang,

Snædís H. Björnsdóttir

et al.

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: July 14, 2020

Geothermal hot springs are a natural setting to study microbial adaptation wide range of temperatures reaching up boiling. Temperature gradients lead distinct communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80-100 ºC) in Yellowstone and Iceland had cooling outflows whose not been studied previously. The composition sediments mats was determined by DNA sequencing rRNA gene amplicons. Over dozen phyla Archaea Bacteria were identified, representing over 1700 organisms. observed significant non-linear reduction the number taxa as increased from warm (38ºC) At taxonomic levels, community structure similar between springs. identified potential endemism at genus level, especially thermophilic phototrophs, which potentially driven environmental conditions dispersal limitations.

Language: Английский

Citations

71
Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin DOI

Katherine Fullerton,

Matthew O. Schrenk, Mustafa Yücel

et al.

Nature Geoscience, Journal Year: 2021, Volume and Issue: 14(5), P. 301 - 306

Published: April 22, 2021

Language: Английский

Citations

62
Strategy improvements to minimize the drawbacks of geothermal investments by using spherical fuzzy modelling DOI Open Access
Serhat Yüksel, Hasan Dınçer, Serkan Eti

et al.

International Journal of Energy Research, Journal Year: 2022, Volume and Issue: 46(8), P. 10796 - 10807

Published: March 25, 2022

This study aims to evaluate the significant risks in geothermal energy investments. For this purpose, a model is suggested by considering Spherical fuzzy DEMATEL technique. With help of literature examination, eight important are identified for these projects. In following step, their weights calculated so that more risk issues can be understood. Another calculation also performed triangular check consistency analysis results. The results both and techniques similar. most essential same methods demonstrate validity findings. indicate accidents because incorrect design-material use has greatest importance since it highest weight. Moreover, decreased water resources pollution them play role regard. Great attention should paid quality material used facilities. Otherwise, there explosion fire facility. These problems threaten lives many people. process, states have very duties. Some standards determined addition, compliance materials with regulations checked routine inspections. situation will minimize due using poor-quality materials.

Language: Английский

Citations

57
Chemolithoautotroph distributions across the subsurface of a convergent margin DOI
Timothy J. Rogers, Joy Buongiorno, Gerdhard L Jessen

et al.

The ISME Journal, Journal Year: 2022, Volume and Issue: 17(1), P. 140 - 150

Published: Oct. 18, 2022

Language: Английский

Citations

41
Building a genome-based understanding of bacterial pH preferences DOI Creative Commons
Josep Ramoneda, Elías Stallard-Olivera, Michael Hoffert

et al.

Science Advances, Journal Year: 2023, Volume and Issue: 9(17)

Published: April 28, 2023

The environmental preferences of many microbes remain undetermined. This is the case for bacterial pH preferences, which can be difficult to predict a priori despite importance as factor structuring communities in systems. We compiled data on distributions from five datasets spanning gradients soil and freshwater systems (1470 samples), quantified taxa across these datasets, genomic representative taxa. While taxonomic phylogenetic information were generally poor predictors we identified genes consistently associated with preference environments. then developed validated machine learning model estimate alone, that could aid selection microbial inoculants, improve species distribution models, or help design effective cultivation strategies. More generally, demonstrate value combining biogeographic infer diverse

Language: Английский

Citations

41