Global diversity of microbial communities in marine sediment

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(44), P. 27587 - 27597

Published: Oct. 19, 2020

Significance Marine sediment covers 70% of Earth’s surface and harbors as much biomass seawater. However, the global taxonomic diversity marine sedimentary communities, spatial distribution that remain unclear. We investigated microbial composition from 40 globally distributed sampling locations, spanning depths 0.1 to 678 m. Statistical analysis reveals oxygen presence or absence organic carbon concentration are key environmental factors for defining communities. Global richness predicted by species–area relationship models is 7.85 × 10 3 6.10 5 Archaea 3.28 4 2.46 6 Bacteria amplicon sequence variants, which comparable in seawater topsoil.

Language: Английский

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Dormancy in the origin, evolution and persistence of life on Earth

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2038)

Published: Jan. 1, 2025

Life has existed on Earth for most of the planet’s history, yet major gaps and unresolved questions remain about how it first arose persisted. Early posed numerous challenges life, including harsh fluctuating environments. Today, many organisms cope with such conditions by entering a reversible state reduced metabolic activity, phenomenon known as dormancy. This process protects inactive individuals minimizes risk extinction preserving information that stabilizes life-system dynamics. Here, we develop framework understanding dormancy early Earth, beginning primer theory its core criteria. We hypothesize dormancy-like mechanisms acting chemical precursors in prebiotic world may have facilitated origin life. Drawing evidence from phylogenetic reconstructions fossil record, demonstrate is prevalent across tree life throughout deep time. These observations lead us to consider might shaped nascent living systems buffering stochastic processes small populations, protecting against large-scale planetary disturbances, aiding dispersal patchy landscapes facilitating adaptive radiations. Given fundamental easily evolved property also likely be feature elsewhere universe.

Language: Английский

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Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 28, 2020

Abstract Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of oligotrophic South Pacific Gyre (SPG). The physiological status these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members communities SPG sediments (4.3‒101.5 Ma) are capable readily incorporating carbon and nitrogen substrates dividing. Most 6986 individual cells analyzed with nanometer-scale secondary ion mass spectrometry (NanoSIMS) actively incorporated isotope-labeled substrates. Many responded rapidly incubation conditions, increasing total numbers by 4 orders magnitude taking up labeled within 68 days after incubation. response was generally faster (on average, 3.09 times) for incorporation than incorporation. In contrast, anaerobic microbes were only minimally revived this sediment. Our results suggest widely distributed organic-poor abyssal consist mainly aerobes retain metabolic potential under extremely low-energy conditions 101.5 Ma.

Language: Английский

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Temperature limits to deep subseafloor life in the Nankai Trough subduction zone

Science, Journal Year: 2020, Volume and Issue: 370(6521), P. 1230 - 1234

Published: Dec. 4, 2020

Deep, hot, and more alive than we thought Marine sediments represent a massive microbial ecosystem, but still do not fully understand what factors shape limit life underneath the seafloor. Analyzing samples from subduction zone off coast of Japan, Heuer et al. found that life, in particular bacterial vegetative cells, decreases as depth temperature increases down to ∼600 meters below seafloor, corresponding temperatures ∼70°C. Below this limit, endospores are common—a remnant, potential reservoir, life. Deeper is sterile zone, 1000 scalding realm populated by cells. At such great depths, high concentrations acetate sulfate coexist, there also signs hyperthermophilic methanogenesis. These data provide fascinating window into an extreme inhospitable environment nonetheless supports Science , issue p. 1230

Language: Английский

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Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms

Marine Life Science & Technology, Journal Year: 2020, Volume and Issue: 3(2), P. 189 - 203

Published: May 13, 2020

Abstract Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in late nineteenth century. However, even today, majority microorganisms marine environment remain uncultivated. There are various explanations for inability to culture laboratory, including lack essential nutrients, osmotic support or incubation conditions, low growth rate, development micro-colonies, and presence senescent viable but nonculturable (VBNC) cells. In environment, many have associated with dormancy, as typified by VBNC state. refers a state where metabolically active, no longer culturable on routine media. It is apparently unique survival strategy that adopted response harsh environmental conditions bacterial cells may regain culturability under favorable conditions. The resuscitation well be an important way cultivate otherwise uncultured environments. Many stimuli promote restoration so far identified; these include sodium pyruvate, quorum sensing autoinducers, resuscitation-promoting factors Rpfs YeaZ, catalase. this review, we focus issues culturability, diversity entering state, mechanisms induction into implications cultivating microorganisms. Bringing still era high-throughput sequencing their ecological functions can often only known through isolation cultivation.

Language: Английский

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Principles of seed banks and the emergence of complexity from dormancy

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Aug. 10, 2021

Abstract Across the tree of life, populations have evolved capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise multi-scale structures networks spanning collections cells entire ecosystems. We outline fundamental attributes emergent phenomena associated dormancy banks, vision for unifying mathematically based framework can address problems life sciences, ranging from global change cancer biology.

Language: Английский

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Formation mechanisms of viable but nonculturable bacteria through induction by light-based disinfection and their antibiotic resistance gene transfer risk: A review

Critical Reviews in Environmental Science and Technology, Journal Year: 2021, Volume and Issue: 52(20), P. 3651 - 3688

Published: June 4, 2021

Disinfection technologies, especially light-based disinfection, have undergone tremendous development and innovation, but this treatment can cause bacteria to enter viable nonculturable (VBNC) state. Due their strong tolerance, VBNC cannot be completely removed by disinfection thereby posing a potential risk for antibiotic resistance gene (ARG) transfer. Therefore, better understand interpret transfer of ARGs, article systematically reviewed changes in morphology, physiology virulence after entering In addition, quantitative detection methods bacteria, such as cell membrane integrity-mediated LIVE/DEAD Baclight assay, qPCR-based assays, phage-based methods, concluding that there is still lack in-situ real-time bacteria. Health risks environmental application value were then valuated, with data indicating great the domain microbial utilization. Furthermore, induction conditions (especially disinfection) formation mechanisms highlighted. Formation mainly involve stringent response, general stress response system toxin-antitoxin (TA) system. Moreover, horizontal (HGT) ARGs during induced was evaluated. It found may transferred through conjugation, transformation transduction. Finally, current deficiencies future challenges those influenced summarized. This review provides new insights into mechanisms, applications ARG

Language: Английский

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Sulfur Biogeochemical Cycle of Marine Sediments

Geochemical Perspectives, Journal Year: 2021, Volume and Issue: unknown, P. 145 - 307

Published: Oct. 1, 2021

Complex interactions between microbial communities and geochemical processes drive the major element cycles control function of marine sediments as a dynamic reservoir organic matter. Sulfate reduction is globally dominant pathway anaerobic mineralisation main source sulfide. The effective re-oxidation this sulfide at direct or indirect expense oxygen prerequisite for aerobic life on our planet. Although largely hidden beneath oxic sediment surface, sulfur cycle therefore critical Earth’s redox state. This Geochemical Perspectives begins with brief primer description my own scientific journey through nearly fifty years studies geochemistry microbiology. Among objectives these were to quantify identify behind them. Radiotracers in combination chemical analyses have thereby been used extensively laboratory experiments, supported by diverse molecular microbiological methods. following sections discuss sulfate reduction, oxidation disproportionation inorganic intermediates, especially elemental thiosulfate. experimental approaches enable analysis how environmental factors such substrate concentration temperature affect process rates concurrent cryptic cycle. energy chemolithotrophic bacteria, including fascinating big bacteria cable supports their dark CO2 fixation, which produces new biomass. During burial aging sediments, predominant change cascade reactions, rate matter degradation drops continuously over many orders magnitude. pathways age turnover are discussed. In deep methanic zone, only few percent entire remains, provides small boost methane oxidation. stable isotopes provide an additional tool understand diagenetic processes, whereby isotope fractionation open system diagenesis generate differential diffusion flux isotopes. relation carbon seabed contribution methane, paper discusses global budget role different depth regions ocean – from coast sea. published estimates parameters evaluated compared. Finally, looks future perspectives respect gaps current understanding need further studies.

Language: Английский

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Microbial population dynamics and evolutionary outcomes under extreme energy limitation

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(33)

Published: Aug. 12, 2021

Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders magnitude 105 y. Our findings corroborate reports long-lived bacteria recovered ancient environmental samples, while providing mechanisms persistence. As death rates declined time, lifespan was extended through the scavenging dead cells. Although suppressed absence exogenous resources, continued evolve. Hundreds mutations were acquired, contributing genome-wide signatures purifying selection as well molecular signals adaptation. Consistent ecological evolutionary dynamics indicate that distantly related respond energy limitation similar predictable manner, which likely contributes stability robustness microbial life.

Language: Английский

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The microbial dimension of submarine groundwater discharge: current challenges and future directions

FEMS Microbiology Reviews, Journal Year: 2021, Volume and Issue: 45(5)

Published: Jan. 28, 2021

ABSTRACT Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, microbial dimension SGD remains poorly understood. can influence marine communities through supplying chemical compounds and microorganisms, in turn, microbes at land–ocean transition zone determine chemistry reaching ocean. However, compared with inland groundwater, little is known about coastal aquifers. Here, we review state art SGD, emphasis on prokaryotes, identify current challenges future directions. Main include improving diversity description microbiota, characterized by ultrasmall, inactive novel taxa, high ratios sediment-attached versus free-living cells. Studies should explore dynamics their role cycles aquifers, bidirectional dispersal seawater bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization linking taxonomy activity but also considering entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, ecology) are needed frame study terrestrial aquatic microorganisms beyond limits presumed habitats, foster our understanding processes biogeochemical cycles.

Language: Английский

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