2020
Sharrar, A. M.; Crits-Christoph, A.; Méheust, R.; Diamond, S.; Starr, E. P.; Banfield, J. F.
Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type. Journal Article
In: mBio, vol. 11, pp. e00416-20, 2020.
Abstract | Links | BibTeX | Tags: ERCZO, metagenomics, secondary metabolism, soil microbiology
@article{Sharrar2020,
title = {Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type.},
author = {A. M. Sharrar and A. Crits-Christoph and R. Méheust and S. Diamond and E. P. Starr and J. F. Banfield},
url = {https://mbio.asm.org/content/11/3/e00416-20},
doi = {10.1128/mBio.00416-20},
year = {2020},
date = {2020-06-16},
journal = {mBio},
volume = {11},
pages = {e00416-20},
abstract = {Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy.},
keywords = {ERCZO, metagenomics, secondary metabolism, soil microbiology},
pubstate = {published},
tppubtype = {article}
}
Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy.
2019
Diamond, Spencer; Andeer, Peter F.; Li, Zhou; Crits-Christoph, Alexander; Burstein, David; Anantharaman, Karthik; Lane, Katherine R.; Thomas, Brian C.; Pan, Chongle; Northen, Trent R.; Banfield, Jillian F.
Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Journal Article
In: Nature Microbiology, vol. 4, pp. 1356-1367, 2019.
Abstract | Links | BibTeX | Tags: ERCZO, metagenomics, soil microbes
@article{Diamond2019,
title = {Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.},
author = {Spencer Diamond and Peter F. Andeer and Zhou Li and Alexander Crits-Christoph and David Burstein and Karthik Anantharaman and Katherine R. Lane and Brian C. Thomas and Chongle Pan and Trent R. Northen and Jillian F. Banfield},
url = {https://angelo.berkeley.edu/wp-content/uploads/sites/59/41564_2019_Article_449.pdf},
doi = {10.1038/s41564-019-0449-y},
year = {2019},
date = {2019-05-20},
journal = {Nature Microbiology},
volume = {4},
pages = {1356-1367},
abstract = {Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.},
keywords = {ERCZO, metagenomics, soil microbes},
pubstate = {published},
tppubtype = {article}
}
Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.
2017
Bouma-Gregson, Keith
The Ecology of Benthic Toxigenic Anabaena and Phormidium (Cyanobacteria) in the Eel River, California PhD Thesis
University of California, Berkeley, 2017, ISBN: 978-0-355-94920-9.
Abstract | BibTeX | Tags: Anabaena, Anatoxin-a, Biological sciences, cyanobacteria, Cyanotoxin, ERCZO, metagenomics, Phormidium
@phdthesis{Bouma-Gregson2017c,
title = {The Ecology of Benthic Toxigenic Anabaena and Phormidium (Cyanobacteria) in the Eel River, California},
author = {Keith Bouma-Gregson},
isbn = {978-0-355-94920-9},
year = {2017},
date = {2017-12-31},
school = {University of California, Berkeley},
abstract = {Cyanobacteria are ubiquitous in aquatic ecosystems across the earth. In many environments they are present at low abundances, however under certain environmental conditions cyanobacteria bloom and become one of the dominant organisms in an waterbody, degrading aquatic food webs and water quality. Cyanobacteria evolved over 2 billion years ago, and cyanobacterial harmful algal blooms (cyanoHABs) have been documented for decades. Of particular concern is the production of cyanotoxins, secondary metabolites toxic to humans and other organisms, by certain strains of cyanobacteria. Most research of cyanoHABs has been of planktonic blooms in lakes or estuaries, and cyanotoxin production by benthic cyanobacteria in rivers has been more recent, but in many rivers benthic cyanobacteria are the primary source of cyanotoxins. With field surveys and monitoring, manipulative field experiments, and genome-resolved metagenomics, this dissertation investigated the ecology of benthic cyanobacteria in the Eel River, California.},
keywords = {Anabaena, Anatoxin-a, Biological sciences, cyanobacteria, Cyanotoxin, ERCZO, metagenomics, Phormidium},
pubstate = {published},
tppubtype = {phdthesis}
}
Cyanobacteria are ubiquitous in aquatic ecosystems across the earth. In many environments they are present at low abundances, however under certain environmental conditions cyanobacteria bloom and become one of the dominant organisms in an waterbody, degrading aquatic food webs and water quality. Cyanobacteria evolved over 2 billion years ago, and cyanobacterial harmful algal blooms (cyanoHABs) have been documented for decades. Of particular concern is the production of cyanotoxins, secondary metabolites toxic to humans and other organisms, by certain strains of cyanobacteria. Most research of cyanoHABs has been of planktonic blooms in lakes or estuaries, and cyanotoxin production by benthic cyanobacteria in rivers has been more recent, but in many rivers benthic cyanobacteria are the primary source of cyanotoxins. With field surveys and monitoring, manipulative field experiments, and genome-resolved metagenomics, this dissertation investigated the ecology of benthic cyanobacteria in the Eel River, California.
2016
Butterfield, Cristina N.; Li, Zhou; Andeer, Peter F.; Spaulding, Susan; Thomas, Brian C.; Singh, Andrea; Hettich, Robert L.; Suttle, Kenwyn B.; Probst, Alexander J.; Tringe, Susannah G.; Northen, Trent; Pan, Chongle; Banfield, Jillian F.
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. Journal Article
In: PeerJ, vol. 4, pp. e2687, 2016.
Abstract | Links | BibTeX | Tags: ERCZO, metagenomics, northern California, soil microbes
@article{Butterfield2016,
title = {Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.},
author = {Cristina N. Butterfield and Zhou Li and Peter F. Andeer and Susan Spaulding and Brian C. Thomas and Andrea Singh and Robert L. Hettich and Kenwyn B. Suttle and Alexander J. Probst and Susannah G. Tringe and Trent Northen and Chongle Pan and Jillian F. Banfield},
url = {https://angelo.berkeley.edu/peerj-2687-2/},
doi = {10.7717/peerj.2687},
year = {2016},
date = {2016-11-08},
journal = {PeerJ},
volume = {4},
pages = {e2687},
abstract = {Annually, half of all plant-derived carbon is added to soil where it is microbially respired to
CO2. However, understanding of the microbiology of this process is limited because most
culture-independent methods cannot link metabolic processes to the organisms present,
and this link to causative agents is necessary to predict the results of perturbations on the
system. We collected soil samples at two sub-root depths (10 – 20 cm and 30 – 40 cm)
before and after a rainfall-driven nutrient perturbation event in a Northern California
grassland that experiences a Mediterranean climate. From ten samples, we reconstructed
198 metagenome-assembled genomes that represent all major phylotypes. We also
quantified 6,835 proteins and 175 metabolites and showed that after the rain event the
concentrations of many sugars and amino acids approach zero at the base of the soil
profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and
Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that
these abundant organisms contribute substantially to carbon turnover in the soil, given
that methylotrophy proteins were among the most abundant proteins in the proteome.
Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in
deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid
degradation. Many of the other bacteria appear to breakdown other components of plant
biomass, as evidenced by the prevalence of various sugar and amino acid transporters and
corresponding hydrolyzing machinery in the proteome. Overall, our work provides
organism-resolved insight into the spatial distribution of bacteria and archaea whose
activities combine to degrade plant-derived organics, limiting the transport of methanol,
amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.},
keywords = {ERCZO, metagenomics, northern California, soil microbes},
pubstate = {published},
tppubtype = {article}
}
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to
CO2. However, understanding of the microbiology of this process is limited because most
culture-independent methods cannot link metabolic processes to the organisms present,
and this link to causative agents is necessary to predict the results of perturbations on the
system. We collected soil samples at two sub-root depths (10 – 20 cm and 30 – 40 cm)
before and after a rainfall-driven nutrient perturbation event in a Northern California
grassland that experiences a Mediterranean climate. From ten samples, we reconstructed
198 metagenome-assembled genomes that represent all major phylotypes. We also
quantified 6,835 proteins and 175 metabolites and showed that after the rain event the
concentrations of many sugars and amino acids approach zero at the base of the soil
profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and
Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that
these abundant organisms contribute substantially to carbon turnover in the soil, given
that methylotrophy proteins were among the most abundant proteins in the proteome.
Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in
deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid
degradation. Many of the other bacteria appear to breakdown other components of plant
biomass, as evidenced by the prevalence of various sugar and amino acid transporters and
corresponding hydrolyzing machinery in the proteome. Overall, our work provides
organism-resolved insight into the spatial distribution of bacteria and archaea whose
activities combine to degrade plant-derived organics, limiting the transport of methanol,
amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.
CO2. However, understanding of the microbiology of this process is limited because most
culture-independent methods cannot link metabolic processes to the organisms present,
and this link to causative agents is necessary to predict the results of perturbations on the
system. We collected soil samples at two sub-root depths (10 – 20 cm and 30 – 40 cm)
before and after a rainfall-driven nutrient perturbation event in a Northern California
grassland that experiences a Mediterranean climate. From ten samples, we reconstructed
198 metagenome-assembled genomes that represent all major phylotypes. We also
quantified 6,835 proteins and 175 metabolites and showed that after the rain event the
concentrations of many sugars and amino acids approach zero at the base of the soil
profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and
Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that
these abundant organisms contribute substantially to carbon turnover in the soil, given
that methylotrophy proteins were among the most abundant proteins in the proteome.
Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in
deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid
degradation. Many of the other bacteria appear to breakdown other components of plant
biomass, as evidenced by the prevalence of various sugar and amino acid transporters and
corresponding hydrolyzing machinery in the proteome. Overall, our work provides
organism-resolved insight into the spatial distribution of bacteria and archaea whose
activities combine to degrade plant-derived organics, limiting the transport of methanol,
amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.