1
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Ali F. Patterns of Change in Nucleotide Diversity Over Gene Length. Genome Biol Evol 2024; 16:evae078. [PMID: 38608148 PMCID: PMC11040516 DOI: 10.1093/gbe/evae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity-length correlation and highlight that selective constraints on the 5'-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on "silent-site" diversity.
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Affiliation(s)
- Farhan Ali
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
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2
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Fullerton H, Smith L, Enriquez A, Butterfield D, Wheat CG, Moyer CL. Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities. FEMS Microbiol Ecol 2024; 100:fiae001. [PMID: 38200713 PMCID: PMC10808952 DOI: 10.1093/femsec/fiae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/20/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.
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Affiliation(s)
- Heather Fullerton
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - Lindsey Smith
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
| | - Alejandra Enriquez
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - David Butterfield
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington and NOAA/PMEL, John M. Wallace Hall, 3737 Brooklyn Ave NE, Seattle, WA 98105, United States
| | - C Geoffrey Wheat
- Institute of Marine Studies, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, 245 O’Neill Building, PO Box 757220, Fairbanks, Alaska 99775-7220, United States
| | - Craig L Moyer
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
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3
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Hampel JJ, Moseley RD, Hamdan LJ. Microbiomes respond predictably to built habitats on the seafloor. Mol Ecol 2023; 32:6686-6695. [PMID: 35567341 DOI: 10.1111/mec.16504] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 04/14/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
Abstract
The seafloor contains complex ecosystems where habitat heterogeneity influences biodiversity. Natural biological and geological features including vents, seeps and reefs create habitats that select for distinct populations of micro- and macrofauna. While largely studied for macrobiological diversity, built habitats may also select distinct microbiomes. Built habitat density on the seafloor is increasing with ocean sprawl expanding in the continental shelf and slope, potentially having widespread effects on benthic communities. This study addresses one type of built habitat, shipwrecks, on microbiomes in surrounding sediment. Using deep-sea sediment samples (762 total) from the Gulf of Mexico, we report elevated diversity and a predictable core microbiome around nine shipwrecks. We show the sphere of influence of built habitats extends up to 300 m onto the seafloor. Supervised learning made predictions of sample proximity to structures based on frequency of taxa. Strongest predictions occurred in sediments nearest and furthest from sites for archaea and mid-transect for bacteria. The response of archaea to built habitats was consistent across sites, while bacteria showed greater between site variability. The archaeal core shipwreck microbiome was enriched in taxa (e.g., Bathyarchaeia, Lokiarchaeia, Thermoplasmata) not present in the surrounding seafloor. Shipwrecks shaped microbiomes in expected ways, providing insight on how built habitats impact microbiome biodiversity in the Anthropocene.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Rachel D Moseley
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
| | - Leila J Hamdan
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
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4
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Li Y, Wang S, Ji B, Yuan Q, Wei S, Lai Q, Wu K, Jiang L, Shao Z. Sulfurovum mangrovi sp. nov., an obligately chemolithoautotrophic, hydrogen-oxidizing bacterium isolated from coastal marine sediments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917543 DOI: 10.1099/ijsem.0.006142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A novel mesophilic, chemolithoautotrophic, hydrogen-oxidizing bacterium, designated strain ST1-3T, was isolated from mud sediment samples collected from mangroves in Jiulong River estuary. The cells were Gram-stain-negative, non-motile and rod-shaped. The temperature, pH and salinity ranges for growth of strain ST1-3T were 4-45 °C (optimum, 35 °C), pH 5.0-8.5 (optimum, pH 7.0) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen as the only energy source, and molecular oxygen, thiosulphate and elemental sulphur as electron acceptors. The major cellular fatty acids of strain ST1-3T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c). The major polar lipids were phosphatidylethanolamine, phosphatidyldimethyl ethanolamine and phosphatidylglycerol. The respiratory quinone was menaquinone-6. The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurovum and was most closely related to Sulfurovum lithotrophicum 42BKTT (94.7 % sequence identity). The average nucleotide identity and digital DNA-DNA hybridization values between ST1-3T and S. lithotrophicum 42BKTT were 74.6 and 16.3 %, respectively. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain ST1-3T represents a novel species of the genus Sulfurovum, for which the name Sulfurovum mangrovi sp. nov. is proposed, with the type strain ST1-3T (=MCCC M25234T=KCTC 25639T).
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Affiliation(s)
- Yufei Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Shasha Wang
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Bowen Ji
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Qing Yuan
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Shiping Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Qiliang Lai
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Kaiyue Wu
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Lijing Jiang
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
- School of Marine Biology, Xiamen Ocean Vocational College, Xiamen, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
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5
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Mateos K, Chappell G, Klos A, Le B, Boden J, Stüeken E, Anderson R. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth. SCIENCE ADVANCES 2023; 9:eade4847. [PMID: 37418533 PMCID: PMC10328410 DOI: 10.1126/sciadv.ade4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/06/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.
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Affiliation(s)
- Katherine Mateos
- Carleton College, Northfield, MN, USA
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Garrett Chappell
- Carleton College, Northfield, MN, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aya Klos
- Carleton College, Northfield, MN, USA
| | - Bryan Le
- Carleton College, Northfield, MN, USA
| | - Joanne Boden
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Eva Stüeken
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Rika Anderson
- Carleton College, Northfield, MN, USA
- NASA NExSS Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
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6
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Batarseh TN, Batarseh SN, Morales-Cruz A, Gaut BS. Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history. Front Microbiol 2023; 14:1206094. [PMID: 37434713 PMCID: PMC10330825 DOI: 10.3389/fmicb.2023.1206094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/09/2023] [Indexed: 07/13/2023] Open
Abstract
'Candidatus Liberibacter' is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the 'Ca. Liberibacter solanacearum' species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the 'Ca. L. capsica' species based on high values of dN.
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Affiliation(s)
| | - Sarah N. Batarseh
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, United States
| | - Abraham Morales-Cruz
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, United States
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7
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Webb EA, Held NA, Zhao Y, Graham ED, Conover AE, Semones J, Lee MD, Feng Y, Fu FX, Saito MA, Hutchins DA. Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades. ISME COMMUNICATIONS 2023; 3:15. [PMID: 36823453 PMCID: PMC9950141 DOI: 10.1038/s43705-023-00214-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/13/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]
Abstract
The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.
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Affiliation(s)
- Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Noelle A Held
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Environmental Systems Science, ETH, Zurich, Switzerland
| | - Yiming Zhao
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Elaina D Graham
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Asa E Conover
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jake Semones
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, NASA Ames Research Center, Mountain View, CA, 94035, USA
| | - Yuanyuan Feng
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mak A Saito
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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8
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Li T, Yin Y. Critical assessment of pan-genomic analysis of metagenome-assembled genomes. Brief Bioinform 2022; 23:6702672. [PMID: 36124775 PMCID: PMC9677465 DOI: 10.1093/bib/bbac413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/30/2022] Open
Abstract
Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.
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Affiliation(s)
- Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, 68508, USA
| | - Yanbin Yin
- Corresponding author. Yanbin Yin, Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68508, USA. Tel.: +1-402-472-4303; E-mail:
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9
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Abstract
The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a 2-year, high-resolution environmental time series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggest that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.
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10
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Zhang X, Liu Z, Xu W, Pan J, Huang Y, Cai M, Luo Z, Li M. Genomic insights into versatile lifestyle of three new bacterial candidate phyla. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1547-1562. [PMID: 35060074 DOI: 10.1007/s11427-021-2037-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/01/2021] [Indexed: 05/28/2023]
Abstract
Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria.
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Affiliation(s)
- Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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11
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Preska Steinberg A, Lin M, Kussell E. Core genes can have higher recombination rates than accessory genes within global microbial populations. eLife 2022; 11:78533. [PMID: 35801696 PMCID: PMC9444244 DOI: 10.7554/elife.78533] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/30/2022] [Indexed: 11/24/2022] Open
Abstract
Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. However, assessing the impact of homologous recombination on accessory genes which are only present in a subset of strains of a given species remains challenging due to their complex phylogenetic relationships. Quantifying homologous recombination for accessory genes (which are important for niche-specific adaptations) in comparison to core genes (which are present in all strains and have essential functions) is critical to understanding how selection acts on variation to shape species diversity and genome structures of bacteria. Here, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome using >100,000 whole genome sequences from Streptococcus pneumoniae and several additional species. By analyzing diverse sets of sequence clusters, we show that core genes often have higher recombination rates than accessory genes, and for some bacterial species the associated effect sizes for these differences are pronounced. In a subset of species, we find that gene frequency and homologous recombination rate are positively correlated. For S. pneumoniae and several additional species, we find that while the recombination rate is higher for the core genome, the mutational divergence is lower, indicating that divergence-based homologous recombination barriers could contribute to differences in recombination rates between the core and accessory genome. Homologous recombination may therefore play a key role in increasing the efficiency of selection in the most conserved parts of the genome.
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Affiliation(s)
| | - Mingzhi Lin
- Department of Biology, New York University, New York, United States
| | - Edo Kussell
- Department of Biology, New York University, New York, United States
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12
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Romero Picazo D, Werner A, Dagan T, Kupczok A. Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance. Genome Biol Evol 2022; 14:evac098. [PMID: 35731940 PMCID: PMC9260185 DOI: 10.1093/gbe/evac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared with core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent HGT between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.
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Affiliation(s)
- Devani Romero Picazo
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
| | - Almut Werner
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
| | - Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Bioinformatics Group, Wageningen University & Research, 6708PB Wageningen, The Netherlands
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13
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Cooper ZS, Rapp JZ, Shoemaker AMD, Anderson RE, Zhong ZP, Deming JW. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Front Microbiol 2022; 13:879116. [PMID: 35733954 PMCID: PMC9207381 DOI: 10.3389/fmicb.2022.879116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
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Affiliation(s)
- Zachary S. Cooper
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
- *Correspondence: Zachary S. Cooper, , orcid.org/0000-0001-6515-7971
| | - Josephine Z. Rapp
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
- Institute of Integrative Biology and Systems (IBIS), Université Laval, Québec, QC, Canada
| | - Anna M. D. Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, United States
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W. Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
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14
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Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis. Microorganisms 2022; 10:microorganisms10040724. [PMID: 35456775 PMCID: PMC9032823 DOI: 10.3390/microorganisms10040724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 02/04/2023] Open
Abstract
Halophilic sulfur-oxidizing bacteria belonging to the genus Guyparkeria occur at both marine and terrestrial habitats. Common physiological characteristics displayed by Guyparkeria isolates have not yet been linked to the metabolic potential encoded in their genetic inventory. To provide a genetic basis for understanding the metabolism of Guyparkeria, nine genomes were compared to reveal the metabolic capabilities and adaptations. A detailed account is given on Guyparkeria’s ability to assimilate carbon by fixation, to oxidize reduced sulfur, to oxidize thiocyanate, and to cope with salinity stress.
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15
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Rolando JL, Kolton M, Song T, Kostka JE. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA. MICROBIOME 2022; 10:37. [PMID: 35227326 PMCID: PMC8886783 DOI: 10.1186/s40168-021-01187-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. RESULTS A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora. CONCLUSIONS The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.
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Affiliation(s)
- Jose L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Max Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, Israel
| | - Tianze Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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16
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Cummins EA, Hall RJ, McInerney JO, McNally A. Prokaryote pangenomes are dynamic entities. Curr Opin Microbiol 2022; 66:73-78. [PMID: 35104691 DOI: 10.1016/j.mib.2022.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/24/2022]
Abstract
Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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17
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Li X, Yang Z, Wang Z, Li W, Zhang G, Yan H. Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity. Front Microbiol 2022; 12:755874. [PMID: 35095786 PMCID: PMC8792951 DOI: 10.3389/fmicb.2021.755874] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas stutzeri is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 P. stutzeri complex genomes covering at least six well-defined species among all sequenced Pseudomonas genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the P. stutzeri complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster (ect) was present in all genomes of P. stutzeri species complex strains but distributed at very low frequency (43 out of 9548) in other Pseudomonas genomes, suggesting a possible origin of the ancestors of P. stutzeri species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the P. stutzeri complex, shedding new light on its genomic diversity and evolutionary history.
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Affiliation(s)
- Xiangyang Li
- School of Sciences, Kaili University, Kaili, China
- Bacterial Genome Data Mining and Bioinformatic Analysis Center, Kaili University, Kaili, China
- *Correspondence: Xiangyang Li,
| | - Zilin Yang
- School of Sciences, Kaili University, Kaili, China
| | - Zhao Wang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Weipeng Li
- School of Big Data Engineering, Kaili University, Kaili, China
| | - Guohui Zhang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Hongguang Yan
- School of Life and Health Science, Kaili University, Kaili, China
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18
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Baecklund TM, Donaldson ME, Hueffer K, Kyle CJ. Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations. PLoS One 2021; 16:e0258975. [PMID: 34714859 PMCID: PMC8555846 DOI: 10.1371/journal.pone.0258975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/10/2021] [Indexed: 11/24/2022] Open
Abstract
Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. FST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- * E-mail:
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- Forensic Science Department, Trent University, Peterborough, ON, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, ON, Canada
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19
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Hoffert M, Anderson RE, Reveillaud J, Murphy LG, Stepanauskas R, Huber JA. Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems. Front Microbiol 2021; 12:714920. [PMID: 34489903 PMCID: PMC8417812 DOI: 10.3389/fmicb.2021.714920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
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Affiliation(s)
- Michael Hoffert
- Biology Department, Carleton College, Northfield, MN, United States.,Finch Therapeutics Group, Somerville, MA, United States
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, MN, United States
| | - Julie Reveillaud
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Montpellier, France
| | | | | | - Julie A Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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20
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Abstract
The deep marine subsurface constitutes a massive biosphere that hosts a multitude of archaea, bacteria, and viruses across a diversity of habitats. These microbes play key roles in mediating global biogeochemical cycles, and the marine subsurface is thought to have been among the earliest habitats for life on Earth. Yet we have a poor understanding of what forces govern the evolution of subsurface microbes over time. Here, I outline why evolutionary trajectories in the subsurface may be different than those of microbes living on the surface of the planet and describe how we can take advantage of technological advancements to study the evolutionary dynamics of subsurface microbes and their viruses. The sequencing revolution, in tandem with marine infrastructure advancements, promises that we will soon gain a much deeper understanding of how the vast majority of the microbial biosphere changes, adapts, and evolves over time.
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21
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Dong X, Zhang C, Li W, Weng S, Song W, Li J, Wang Y. Functional diversity of microbial communities in inactive seafloor sulfide deposits. FEMS Microbiol Ecol 2021; 97:6327547. [PMID: 34302348 DOI: 10.1093/femsec/fiab108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/22/2021] [Indexed: 11/12/2022] Open
Abstract
The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.
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Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Wenli Li
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Weizhi Song
- Centre for Marine Science & Innovation, University of New South Wales, 2052 Sydney, Australia
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Yong Wang
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
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22
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Abstract
In the ocean, viruses impact microbial mortality, regulate biogeochemical cycling, and alter the metabolic potential of microbial lineages. At deep-sea hydrothermal vents, abundant viruses infect a wide range of hosts among the archaea and bacteria that inhabit these dynamic habitats. However, little is known about viral diversity, host range, and biogeography across different vent ecosystems, which has important implications for how viruses manipulate microbial function and evolution. Here, we examined viral diversity, viral and host distribution, and virus-host interactions in microbial metagenomes generated from venting fluids from several vent sites within three different geochemically and geographically distinct hydrothermal systems: Piccard and Von Damm vent fields at the Mid-Cayman Rise in the Caribbean Sea, and at several vent sites within Axial Seamount in the Pacific Ocean. Analysis of viral sequences and clustered regularly interspaced short palindromic repeat (CRISPR) spacers revealed highly diverse viral assemblages and evidence of active infection. Network analysis revealed that viral host range was relatively narrow, with very few viruses infecting multiple microbial lineages. Viruses were largely endemic to individual vent sites, indicating restricted dispersal, and in some cases, viral assemblages persisted over time. Thus, we show that hydrothermal vent fluids are home to novel, diverse viral assemblages that are highly localized to specific regions and taxa. IMPORTANCE Viruses play important roles in manipulating microbial communities and their evolution in the ocean, yet not much is known about viruses in deep-sea hydrothermal vents. However, viral ecology and evolution are of particular interest in hydrothermal vent habitats because of their unique nature: previous studies have indicated that most viruses in hydrothermal vents are temperate rather than lytic, and it has been established that rates of horizontal gene transfer (HGT) are particularly high among thermophilic vent microbes, and viruses are common vectors for HGT. If viruses have broad host range or are widespread across vent sites, they have increased potential to act as gene-sharing "highways" between vent sites. By examining viral diversity, distribution, and infection networks across disparate vent sites, this study provides the opportunity to better characterize and constrain the viral impact on hydrothermal vent microbial communities. We show that viruses in hydrothermal vents are diverse and apparently active, but most have restricted host range and are not widely distributed among vent sites. Thus, the impacts of viral infection are likely to be highly localized and constrained to specific taxa in these habitats.
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23
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N'Guessan A, Brito IL, Serohijos AWR, Shapiro BJ. Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures. Genome Biol Evol 2021; 13:6300526. [PMID: 34132784 PMCID: PMC8358218 DOI: 10.1093/gbe/evab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Pangenomes—the cumulative set of genes encoded by a population or species—arise from the interplay of horizontal gene transfer, drift, and selection. The balance of these forces in shaping pangenomes has been debated, and studies to date focused on ancient evolutionary time scales have suggested that pangenomes generally confer niche adaptation to their bacterial hosts. To shed light on pangenome evolution on shorter evolutionary time scales, we inferred the selective pressures acting on mobile genes within individual human microbiomes from 176 Fiji islanders. We mapped metagenomic sequence reads to a set of known mobile genes to identify single nucleotide variants (SNVs) and calculated population genetic metrics to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation without the need to invoke the adaptive value of mobile genes to either bacterial or human hosts. These results stand in contrast with the apparent adaptive value of pangenomes over longer evolutionary time scales. In general, the most highly mobile genes (i.e., those present in more distinct bacterial host genomes) tend to have higher metagenomic read coverage and an excess of low-frequency SNVs, consistent with their rapid spread across multiple bacterial species in the gut. However, a subset of mobile genes—including those involved in defense mechanisms and secondary metabolism—showed a contrasting signature of intermediate-frequency SNVs, indicating species-specific selective pressures or negative frequency-dependent selection on these genes. Together, our evolutionary models and population genetic data show that gene-specific selective pressures predominate over human or bacterial host-specific pressures during the relatively short time scales of a human lifetime.
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Affiliation(s)
- Arnaud N'Guessan
- Departement de Biochimie, Université de Montréal, Québec, Canada.,Centre Robert-Cedergren en Bio-informatique et Génomique, Université de Montréal, Québec, Canada
| | - Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Adrian W R Serohijos
- Departement de Biochimie, Université de Montréal, Québec, Canada.,Centre Robert-Cedergren en Bio-informatique et Génomique, Université de Montréal, Québec, Canada
| | - B Jesse Shapiro
- Département de Sciences Biologiques, Complexe des Sciences, Université de Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Québec, Canada.,McGill Genome Centre, Montreal, Québec, Canada
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24
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Allopatric Plant Pathogen Population Divergence following Disease Emergence. Appl Environ Microbiol 2021; 87:AEM.02095-20. [PMID: 33483307 DOI: 10.1128/aem.02095-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the study of plant pathogen populations in monocultures can highlight the distinct evolutionary mechanisms that lead to local genetic differentiation. Xylella fastidiosa is a plant pathogen known to infect and damage multiple monocultures worldwide. One subspecies, Xylella fastidiosa subsp. fastidiosa, was first introduced to the United States ∼150 years ago, where it was found to infect and cause disease in grapevines (Pierce's disease of grapevines, or PD). Here, we studied PD-causing subsp. fastidiosa populations, with an emphasis on those found in the United States. Our study shows that following their establishment in the United States, PD-causing strains likely split into populations on the East and West Coasts. This diversification has occurred via both changes in gene content (gene gain/loss events) and variations in nucleotide sequence (mutation and recombination). In addition, we reinforce the notion that PD-causing populations within the United States acted as the source for subsequent subsp. fastidiosa outbreaks in Europe and Asia.IMPORTANCE Compared to natural environments, the reduced diversity of monoculture agricultural landscapes can lead bacterial plant pathogens to quickly adapt to local biological and ecological conditions. Because of this, accidental introductions of microbial pathogens into naive regions represents a significant economic and environmental threat. Xylella fastidiosa is a plant pathogen with an expanding host and geographic range due to multiple intra- and intercontinental introductions. X. fastidiosa subsp. fastidiosa infects and causes disease in grapevines (Pierce's disease of grapevines [PD]). This study focused on PD-causing X. fastidiosa populations, particularly those found in the United States but also invasions into Taiwan and Spain. The analysis shows that PD-causing X. fastidiosa has diversified via multiple cooccurring evolutionary forces acting at an intra- and interpopulation level. This analysis enables a better understanding of the mechanisms leading to the local adaptation of X. fastidiosa and how a plant pathogen diverges allopatrically after multiple and sequential introduction events.
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Parsons C, Stüeken EE, Rosen CJ, Mateos K, Anderson RE. Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history. GEOBIOLOGY 2021; 19:18-34. [PMID: 33108025 PMCID: PMC7894544 DOI: 10.1111/gbi.12419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen-utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen-cycling genes, dated with a time-calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum-based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid-Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N2 . Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.
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Affiliation(s)
- Chris Parsons
- Carleton CollegeNorthfieldMNUSA
- Massachusetts Institute of TechnologyCambridgeMAUSA
| | | | | | | | - Rika E. Anderson
- Carleton CollegeNorthfieldMNUSA
- NASA NExSS Virtual Planetary LaboratoryUniversity of WashingtonSeattleWAUSA
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