Microbial Community in Hyperalkaline Steel Slag-Fill Emulates Serpentinizing Springs

© 2019 by the authors. To date, a majority of studies of microbial life in hyperalkaline settings focus on environments that are also highly saline (haloalkaline). Haloalkaline conditions offer microbes abundant workarounds to maintain pH homeostasis, as salt ions can be exchanged for protons by dedicated antiporter proteins. Yet hyperalkaline freshwater systems also occur both naturally and anthropogenically, such as the slag fill aquifers around former Lake Calumet (Chicago, IL, USA). In this study, 16S rRNA gene sequences and metagenomic sequence libraries were collected to assess the taxonomic composition and functional potential of microbes present in these slag-polluted waterways. Relative 16S rRNA gene abundances in Calumet sediment and water samples describe community compositions not significantly divergent from those in nearby circumneutral conditions. Major differences in composition are mainly driven by Proteobacteria, primarily one sequence cluster closely related to Hydrogenophaga, which comprises up to 85% of 16S rRNA gene abundance in hyperalkaline surface sediments. Sequence identity indicates this novel species belongs to the recently established genus Serpentinomonas, a bacterial lineage associated with natural freshwater hyperalkaline serpentinizing springs

Biogeography of American Northwest Hot Spring A/B′-Lineage Synechococcus Populations

© Copyright © 2020 Becraft, Wood, Cohan and Ward. Previous analyses have shown how diversity among unicellular cyanobacteria inhabiting island-like hot springs is structured relative to physical separation and physiochemical differences among springs, especially at local to regional scales. However, these studies have been limited by the low resolution provided by the molecular markers surveyed. We analyzed large datasets obtained by high-throughput sequencing of a segment of the photosynthesis gene psaA from samples collected in hot springs from geothermal basins in Yellowstone National Park, Montana, and Oregon, all known from previous studies to contain populations of A/B′-lineage Synechococcus. The fraction of identical sequences was greater among springs separated by 50 km, and springs separated by \u3e800 km shared sequence variants only rarely. Phylogenetic analyses provided evidence for endemic lineages that could be related to geographic isolation and/or geochemical differences on regional scales. Ecotype Simulation 2 was used to predict putative ecotypes (ecologically distinct populations), and their membership, and canonical correspondence analysis was used to examine the geographical and geochemical bases for variation in their distribution. Across the range of Oregon and Yellowstone, geographical separation explained the largest percentage of the differences in distribution of ecotypes (9.5% correlated to longitude; 9.4% to latitude), with geochemical differences explaining the largest percentage of the remaining differences in distribution (7.4–9.3% correlated to magnesium, sulfate, and sulfide). Among samples within the Greater Yellowstone Ecosystem, geochemical differences significantly explained the distribution of ecotypes (6.5–9.3% correlated to magnesium, boron, sulfate, silicon dioxide, chloride, and pH). Nevertheless, differences in the abundance and membership of ecotypes in Yellowstone springs with similar chemistry suggested that allopatry may be involved even at local scales. Synechococcus populations have diverged both by physical isolation and physiochemical differences, and populations on surprisingly local scales have been evolving independently

Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chen, M. L., Becraft, E. D., Pachiadaki, M., Brown, J. M., Jarett, J. K., Gasol, J. M., Ravin, N. V., Moser, D. P., Nunoura, T., Herndl, G. J., Woyke, T., & Stepanauskas, R. Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f. Frontiers in Microbiology, 11, (2020): 376, doi: 10.3389/fmicb.2020.00376.Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.This work was funded by the United States National Science Foundation grants 1460861 (REU site at Bigelow Laboratory for Ocean Sciences), 1441717, 1335810, and 1232982 to RS, and the Simons Foundation (Life Sciences Project Award ID 510023) to RS. NR was supported by the Ministry of Science and Higher Education of Russia. GH was supported by the Austrian Science Fund (FWF) project ARTEMIS (P28781-B21) and the European Research Council under the European Community’s Seventh Framework Program (FP7/2007-2013)/ERC (Grant Agreement No. 268595). JG was supported by Spanish project RTI2018-101025-B-I00. TW and JJ were funded by the U.S. Department of Energy, Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This “microbial dark matter” represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum “Calescamantes” (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.This work was supported by NASA exobiology grant EXO-NNX11AR78G, U.S. National Science Foundation grant OISE 0968421, and U.S. Department of Energy grant DE-EE-0000716. B.P.H. acknowledges generous support from Greg Fullmer through the UNLV Foundation, and W.S. acknowledges Northern Illinois University for funding. B.P.H and S.K.M. acknowledge support from an Amazon Web Services Education Research Grant award. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. This article is made openly accessible in part by an award from the Northern Illinois University Libraries’ Open Access Publishing Fund

Hiding in plain sight: The globally distributed bacterial candidate phylum PAUC34f

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments. © Copyright © 2020 Chen, Becraft, Pachiadaki, Brown, Jarett, Gasol, Ravin, Moser, Nunoura, Herndl, Woyke and Stepanauskas

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

© 2015 Kim, Nowack, Olsen, Becraft, Wood, Thiel, Klapper, Kühl, Fredrickson, Bryant, Ward and Metz. Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of <i>Synechococcus</i> inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

© 2015 Becraft, Wood, Rusch, Kühl, Jensen, Bryant, Roberts, Cohan and Ward. Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same putative ecotype formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the putative ecotypes are ecologically distinct, the members of each ecotype are ecologically homogeneous. Putative ecotypes responded differently to experimental perturbations of temperature and light, but the genetic variation within each putative ecotype was maintained as the relative abundances of putative ecotypes changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to putative ecotypes that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for putative ecotypes that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time

Hydrogen-Based Metabolism as an Ancestral Trait in Lineages Sibling to the Cyanobacteria

© 2019, The Author(s). The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytochromatia, may constrain the metabolic platform in which aerobic respiration arose. Here, we analyze genomic sequences and predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may be able to use O2 under certain conditions via a putative novel type of heme copper O2 reductase. Similarly, Melainabacteria have diverse energy metabolisms and are capable of fermentation and aerobic or anaerobic respiration. The ancestor of all these groups may have been an anaerobe in which fermentation and H2 metabolism were central metabolic features. The ability to use O2 as a terminal electron acceptor must have been subsequently acquired by these lineages

Ancestral absence of electron transport chains in Patescibacteria and DPANN

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548