2021
Tune, AK
Interactions between carbon cycling and bedrock weathering in a forest of the Northern California Coast Ranges PhD Thesis
2021.
BibTeX | Tags: bedrock weathering, carbon flow, ERCZO, mixed evergreen forests, northern California
@phdthesis{Tune2021,
title = {Interactions between carbon cycling and bedrock weathering in a forest of the Northern California Coast Ranges},
author = {AK Tune},
year = {2021},
date = {2021-12-31},
keywords = {bedrock weathering, carbon flow, ERCZO, mixed evergreen forests, northern California},
pubstate = {published},
tppubtype = {phdthesis}
}
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.
2003
Suttle, K. Blake
Burrow use in a northern California population of the wolf spider Schizocosa McCooki Journal Article
In: Journal of Arachnology, vol. 31, no. 3, pp. 433-436, 2003.
Abstract | Links | BibTeX | Tags: Burrow use, lycosids, northern California
@article{Suttle2003b,
title = {Burrow use in a northern California population of the wolf spider Schizocosa McCooki},
author = {K. Blake Suttle},
url = {https://angelo.berkeley.edu/wp-content/uploads/sites/59/BURROW-USE-IN-A-NORTHERN-CALIFORNIA-POPULATION-OF-THE-WOLF-SPIDER-SCHIZOCOSA-MCCOOKI-ARANEAE-LYCOSIDAE_Suttle.pdf},
doi = {http://dx.doi.org/10.1636/0161-8202(2003)031[0433:BUIANC]2.0.CO;2},
year = {2003},
date = {2003-00-00},
journal = {Journal of Arachnology},
volume = {31},
number = {3},
pages = {433-436},
abstract = {Observations on the wolf spider Schizocosa mccooki in northern California grasslands reveal previously unreported burrowing behavior, known to occur in only one other member of the genus. Adult and penultimate female S. mccooki may occupy burrows that vary widely in depth and the occurrence of silk linings. Mark-resight techniques revealed burrow fidelity spanning several weeks for individual spiders. Behaviors such as courtship and prey consumption can occur at, but are not restricted to, the entrances to these burrows. Burrows appear to offer daytime shelter for S. mccooki, though it remains unclear whether protection from predators or amelioration of abiotic conditions is the primary basis for burrow use.},
keywords = {Burrow use, lycosids, northern California},
pubstate = {published},
tppubtype = {article}
}
Observations on the wolf spider Schizocosa mccooki in northern California grasslands reveal previously unreported burrowing behavior, known to occur in only one other member of the genus. Adult and penultimate female S. mccooki may occupy burrows that vary widely in depth and the occurrence of silk linings. Mark-resight techniques revealed burrow fidelity spanning several weeks for individual spiders. Behaviors such as courtship and prey consumption can occur at, but are not restricted to, the entrances to these burrows. Burrows appear to offer daytime shelter for S. mccooki, though it remains unclear whether protection from predators or amelioration of abiotic conditions is the primary basis for burrow use.
2001
Hunter, John C.; Barbour, Michael G.
Through-growth by Pseudotsuga menziesii: A mechanism for change in forest composition without canopy gaps Journal Article
In: Journal of Vegetation Science, vol. 12, no. 4, pp. 445-452, 2001, ISSN: 1100-9233.
Abstract | Links | BibTeX | Tags: acer-saccharum, competition, disturbance, light, morphology, northern California, patterns, recruitment, stands, trees
@article{Hunter2001,
title = {Through-growth by Pseudotsuga menziesii: A mechanism for change in forest composition without canopy gaps},
author = {John C. Hunter and Michael G. Barbour},
url = {https://angelo.berkeley.edu/wp-content/uploads/sites/59/Through-Growth-by-Pseudotsuga-menziesii-A-Mechanism-for-Change-in-Forest-Composition-without-Canopy-Gaps_Hunter_Barbour_2001.pdf},
doi = {10.2307/3236996},
issn = {1100-9233},
year = {2001},
date = {2001-08-00},
journal = {Journal of Vegetation Science},
volume = {12},
number = {4},
pages = {445-452},
abstract = {exception. In California's Pseudotsuga-mixed hardwood forests, crowns of Pseudotsuga menziesii (Douglas fir) are within those of angiosperm trees (Arbutus menziesii and Quercus species). In the forests we examined, every Pseudotsuga was younger and all but one were growing more rapidly in girth than the Arbutus or Quercus whose crown it had penetrated. Furthermore, as saplings. the Pseudotsuga had grown at rates between those of suppressed saplings and canopy dominants, The recruitment of emergent Pseudotsuga substantially alters these canopies because of the large size Pseudotsuga attains. Given the density of Pseudotsuga growing in canopy crowns, such recruitment is likely. As a mechanism of recruitment, this through-growth differs from gap recruitment in that the turnover of canopy trees is determined by an understory species' growth rate rather than the overstory species' longevity, and community attributes may change rapidly by replacement of canopy dominants with a dissimilar species. Pseudotsuga could grow through the canopy because of its greater potential height (> 60m vs. 20-40m for the angio-perms). narrower crown and its branches suffering less mechanical damage than those of the angiosperms. In general, resource levels in the understory, canopy height, and interspecific differences in maximum height and crown architecture all influence the likelihood of through-growth. Therefore, for vegetation types whose dominants differ substantially in growth form, through-growth may be a mechanism for rapid ecosystem change.},
keywords = {acer-saccharum, competition, disturbance, light, morphology, northern California, patterns, recruitment, stands, trees},
pubstate = {published},
tppubtype = {article}
}
exception. In California’s Pseudotsuga-mixed hardwood forests, crowns of Pseudotsuga menziesii (Douglas fir) are within those of angiosperm trees (Arbutus menziesii and Quercus species). In the forests we examined, every Pseudotsuga was younger and all but one were growing more rapidly in girth than the Arbutus or Quercus whose crown it had penetrated. Furthermore, as saplings. the Pseudotsuga had grown at rates between those of suppressed saplings and canopy dominants, The recruitment of emergent Pseudotsuga substantially alters these canopies because of the large size Pseudotsuga attains. Given the density of Pseudotsuga growing in canopy crowns, such recruitment is likely. As a mechanism of recruitment, this through-growth differs from gap recruitment in that the turnover of canopy trees is determined by an understory species’ growth rate rather than the overstory species’ longevity, and community attributes may change rapidly by replacement of canopy dominants with a dissimilar species. Pseudotsuga could grow through the canopy because of its greater potential height (> 60m vs. 20-40m for the angio-perms). narrower crown and its branches suffering less mechanical damage than those of the angiosperms. In general, resource levels in the understory, canopy height, and interspecific differences in maximum height and crown architecture all influence the likelihood of through-growth. Therefore, for vegetation types whose dominants differ substantially in growth form, through-growth may be a mechanism for rapid ecosystem change.