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Yu-Chen Ling and John W. Moreau

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Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. 4 (Ling et al., 2015) Fig. 5 (Ling et al., 2015) Ac8nobacteria 0.0 0.0 Verrucomicrobia Te Tl 0.4 0.8 1.2 Verrucomicrobia0.4 0.8 1.2 These three zones showed similar microbial members but in different abundances, which were controlled by log(DNA(%)+1) Deltaproteobacteria Th Tf log(DNA(%)+1) Deltaproteobacteria environmental parameters. Method D Deltaproteobacteria Fig. 1 Zone 1 Zone 2 Zone 3 Thermoprotei Thermoprotei Method BAlphaproteobacteria Halobacteria Thermoprotei Methanomicrobia Archaeoglobi 1.5 1.5 Ignavibacteria Thermoplasmata Spirochaetes Deferribacteres Gammaproteobacteria Tidal inundation provides a potential economic Deltaproteobacteria Method C Planctomycetacia Halobacteria Deltaproteobacteria Ignavibacteria Spirochaetes Zetaproteobacteria 1.5 Gammaproteobacteria treatment for the CASS issue. Microbial reduction Phycisphaerae Deltaproteobacteria Chloroflexi Chloroflexi Acidobacteria Actinobacteria Crenarchaeota Verrucomicrobia Planctomycetacia Crenarchaeota Gammaproteobacteria Euryarchaeota Chlorobi Methanomicrobia Acidobacteria Spirochaetes contributes to more than 50% of the alkalinity by Actinobacteria Planctomycetes Mollicutes Chlorobi 1.0 1.0 Actinobacteria Proteobacteria Ac2nobacteria generating iron(II) and sulfide, which will combine Planctomycetes 1.0 Acidobacteria Acidobacteria_Gp3 Euryarchaeota Alphaproteobacteria Actinobacteria Archaea Thermotogae Acidobacteria_Gp1 Tenericutes Acidobacteria_Gp1 Betaproteobacteria Acidobacteria Deferribacteres Archaea Zetaproteobacteria and deposit iron sulfide minerals back to the soils. Gammaproteobacteria Epsilonproteobacteria Firmicutes Zetaproteobacteria Alphaproteobacteria Acidobacteria Clostridia log(RNA(%)+1) Firmicutes log(RNA(%)+1) Fusobacteria Fusobacteria log(cDNA(%)+1) Acidobacteria_Gp2 Bacteria However, there is limited knowledge about Bacteria Proteobacteria Bacilli Bacteria Proteobacteria 25 Chloroflexi Gammaproteobacteria Ignavibacteria MethodChloroflexi E 0.5 Bacteroidetes 20 Planctomycetes Anaerolineae Bacteroidetes Sphingobacteria Firmicutes Flavobacteria Spirochaetes Gammaproteobacteria Actinobacteria Bacteroidetes Alphaproteobacteria microbial dynamics in long-term efficiency in the Planctomycetacia 20 Clostridia Bacteroidia Bacteroidetes 0.5 Tenericutes 0.5 Bacilli Chloroflexi 15 Actinobacteria Dehalococcoidetes Actinobacteria Bacteroidetes Bacteroidetes_incertae_sedis Planctomycetes Cyanobacteria Actinobacteria_Acidimicrobiia CASS system. 15 Cyanobacteria,@ Acidobacteria Cyanobacteria_Chloroplast Cyanobacteria,@ Firmicutes_Clostridia Nitrospirae Flavobacteria Firmicutes Chloroplast Ktedonobacteria Bacteroidia Chloroflexi Sphingobacteria Method C 0.0 Chloroplast Acidobacteria 10 Mollicutes 0.4 0.8 1.2 Euryarchaeota Chloroflexi Motivation: Providing detailed information 10 Firmicutes Betaproteobacteria Alphaproteobacteria Sphingobacteria Deltaproteobacteria Crenarchaeota Betaproteobacteria Verrucomicrobia log(DNA(%)+1) Method D Ac8nobacteria Bacteroidetes_incertae_sedis Deltaproteobacteria 5 about microbial distribution and activity patterns Alphaproteobacteria 5 Epsilonproteobacteria Bacteroidia Flavobacteria Planctomycetes Dehalococcoidetes Relative Abundance (%) Relative Abundance (%) Planctomycetes Firmicutes Spirochaetes Firmicutes_Clostridia Sphingobacteria Anaerolineae Alphaproteobacteria Ac8nobacteria 0.0 Acidobacteria for people who want to build up a complete 0 0 Negativicutes 0.0 Dehalococcoidetes Fig. 6 Anaerolineae Clostridia Others Verrucomicrobia Verrucomicrobia Bacteroidetes Zetaproteobacteria Epsilonproteobacteria Bacilli biogeochemical model, which can be used to Epsilonproteobacteria Zone 2 Zone 3 Abundant Zone(Ling 2 etRareZone al., 32015) 0.4 0.8 Gammaproteobacteria1.2 0.4 0.8 1.2 log(DNA(%)+1) Taxa log(DNA(%)+1) Deltaproteobacteria Site C Zone 1, pH < 5.5 Site B Alphaproteobacteria Zone 1, pH < 5.5 Deltaproteobacteria Gammaproteobacteria Fig. 9 Site A predict and evaluate bioremediation long-term For example, Zone 1 contained microorganisms that favor aZone lower 1, pH = 5.5-6.5 pH condition, Zone Zone2 1,contained pH = 5.5-6.5 the most Early Zetaproteobacteria Deltaproteobacteria efficiency or potential land management. sulfate-reducing bacteria. Microbial compositions Fig. 10 Microbial activity (cDNA:DNA) across a tidal_Syntrophobacterales cycle Delayed Color Key Color Key AcidobacteriaActinobacteria Cyanobacteria Actinobacteria_Acidimicrobiia Firmicutes_Clostridia Nitrospirae 7 Early responders Acidobacteria Microorganisms were divided into Euryarchaeota Chloroflexi 25 20 Delayed responders Crenarchaeota Ac2nobacteria -1.5 -0.5 0.5 1.5 6 -1.5 -0.5 0.5 1.5 Study site and methods 20 Value Value Deltaproteobacteria early and delayed responder based Epsilonproteobacteria WS3 Otu0145 Otu0099Otu0177 Otu0430Otu0414 Otu0145 20 Otu0839Otu0301 Otu0099Otu0177 Otu0442Otu0319 Otu0414 Otu0431Otu0502 Otu0301Otu0430 5 Otu0454 Otu0839 Otu0156Otu0781 Otu0319 Firmicutes_Clostridia Otu0232Otu0531 Otu0502Otu0442 Otu0679Otu0226 Otu0454Otu0431 Spirochaetes Otu0001Otu0782 DeltaproteobacteriaOtu0781 Otu0390 Otu0156 15 Otu0917Otu0780 Otu0531 Otu0307Otu0311 Otu0226Otu0232 Study site: East Trinity wetland, Cairns Otu0332Otu0050 Otu0782Otu0679 Otu0629Otu0089 Otu0001 Otu0233Otu0046 Otu0780Otu0390 Otu0331Otu0224 Otu0311Otu0917 Otu0668Otu0140 Otu0307 Firmicutes Otu0050 15 Method D Otu0383Otu0351 Otu0332 Otu0330Otu0123 Otu0089 Otu0042Otu0334 Otu0046Otu0629 Acidobacteria Otu0192Otu0039 Otu0224Otu0233 Verrucomicrobia Otu0035Otu0157 Otu0140Otu0331 on their activity increasing period Otu0284 Otu0085Otu0547 Otu0351Otu0668 Otu0010Otu0299 Otu0383 Acidobacteria Otu0333Otu0269 Otu0330Otu0123 4 Otu0002Otu0187 Otu0334 Otu0208Otu0628 Otu0039Otu0042 Otu0445Otu0294 Otu0157Otu0192 15 Otu0116 Otu0139Otu0094 Otu0284Otu0035 Otu0211Otu0278 Otu0085Otu0547 Otu0096Otu0129 Otu0299 Otu0095Otu0407 Otu0269Otu0010 Otu0281Otu0276 Otu0187Otu0333 Otu0076Otu0259 Otu0002 Otu0470Otu0154 Otu0208Otu0628 Otu0513Otu0439 Otu0294 Otu0619Otu0072 Otu0116Otu0445 1970s-2001: Drainage; Otu0365Otu0678 Otu0094 Otu0066 Otu0139 Otu0214Otu0023 Otu0211Otu0278 Otu0216Otu0041 Otu0096Otu0129 Otu0079Otu0153 Otu0407 Otu0016Otu0125 Otu0276Otu0095 10 Otu0053 AlphaproteobacteriaOtu0281 Planctomycetes Otu0158Otu0469 Otu0259 Otu0009Otu0197 Otu0154Otu0076 3 Otu0132 Otu0470 Otu0623Otu0228 Otu0439 10 Otu0572 Otu0513 (Fig. 11). Then compared the Otu0389 Otu0072 Otu0379Otu0113 56Otu0678Otu0619% Taxa Otu0036Otu0020 Otu0365 _Planctomycetia Otu0180Otu0044 Otu0023Otu0066 Chloroflexi Otu0257 Otu0214 Otu0064Otu0067 Otu0041 Otu0408Otu0115 Otu0153Otu0216 Site C Otu0355Otu0815 Otu0125Otu0079 Deltaproteobacteria 10 Otu0298 Otu0336Otu0325 Otu0053Otu0016 Otu0458Otu0243 Otu0469 Site B Otu0184Otu0485 Otu0197Otu0158 MethodOtu0011Otu0377 E Otu0132Otu0009 Otu0391Otu0287 Otu0228 Alphaproteobacteria Otu0364Otu0777 Otu0572Otu0623 Site A Otu0018Otu0105 Otu0389 Otu0250Otu0199 Otu0379Otu0113 After 2001: Tidal inundation treatment Otu0167Otu0239 Otu0036Otu0020 Gammaproteobacteria Otu0181Otu0783 Otu0044 Otu0321Otu0324 Otu0257Otu0180 2 Otu0477Otu0175 Otu0064Otu0067 Early Otu0005Otu0528 Otu0115 Otu0193Otu0122 Otu0815Otu0408 Otu0809Otu0261 Otu0355 Otu0118Otu0234 Otu0325Otu0298 Otu0003Otu0594 Otu0243Otu0336 Otu0521Otu0416 Otu0458 activity patterns with phylogenetic Otu1008Otu0300 Otu0184Otu0485 Planctomycetes 5 Otu0473 Otu0377 Deltaproteobacteria 5 Otu0317Otu0183 Otu0011 Otu0853Otu0550 Otu0391Otu0287 Otu0616Otu0189 Otu0777 Otu0004Otu0352 Otu0105Otu0364 5 GammaproteobacteriaDelayed Otu0103Otu0006 Otu0199Otu0018 Otu0378Otu0149 Otu0250
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  • Downloaded 13 April 2017); Using Diamond

    Downloaded 13 April 2017); Using Diamond

    bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Re-evaluating the salty divide: phylogenetic specificity of 6 transitions between marine and freshwater systems 7 8 9 10 Sara F. Pavera, Daniel J. Muratorea, Ryan J. Newtonb, Maureen L. Colemana# 11 a 12 Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA 13 b School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA 14 15 Running title: Marine-freshwater phylogenetic specificity 16 17 #Address correspondence to Maureen Coleman, [email protected] 18 bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Marine and freshwater microbial communities are phylogenetically distinct and transitions 21 between habitat types are thought to be infrequent. We compared the phylogenetic diversity of 22 marine and freshwater microorganisms and identified specific lineages exhibiting notably high or 23 low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA 24 gene tag-sequencing datasets. As expected, marine and freshwater microbial communities 25 differed in the relative abundance of major phyla and contained habitat-specific lineages; at the 26 same time, however, many shared taxa were observed in both environments. 27 Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between 28 marine and freshwater sample pairs.
  • Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)

    Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)

    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria.
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X

    Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X

    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae