Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing

Darjany, Lindsay E; Whitcraft, Christine R.; Dillon, Jesse G.

doi:10.3389/fmicb.2014.00263

Cited by 28 publications

(14 citation statements)

References 76 publications

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“…within the Gammaproteobacteria detected in the heavy fraction of the 13 C treatments was the main C utilizer. Some bacterial OTUs from the Myxococcales (Deltaproteobacteria) also appeared to assimilate the various C sources, which is in agreement with previous studies that members of this order are involved in lignocellulose degradation (Darjany et al, 2014) In contrast to the association patterns observed between Proteobacteria and multiple C sources, OTUs belonging to the phylum Bacteroidetes (e.g. the family…”

Section: Taxa-specific Associations With C Sources and Ssd: Do Soils supporting

confidence: 90%

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields

Rime

Hartmann

Stierli

et al. 2016

Soil Biology and Biochemistry

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Microbial communities and soil carbon (C) have been shown to vary in response to increasing vegetation cover during soil development after deglaciation. However, little is known about the ability of microorganisms to utilize various C sources in glacier forefield soils. We supplied ecologically relevant 13 C-labeled C sources (Chlorella, Penicillium and Festuca) to three distinct environments (supraglacial sediments, barren soils and vegetated soils) of the Damma glacier area to monitor 13 CO 2 production. We identified prokaryotic and fungal populations able to utilize these sources by using DNA-stable isotope probing coupled with Illumina MiSeq sequencing of ribosomal markers. A high initial 13 CO 2 pulse indicated that 13 C-labeled microbial and plant material were consumed. The 13 C-enriched DNA results indicated that betaproteobacterial taxa affiliated to the families Oxalobacteraceae and Comamonadaceae were important players in C utilization from different sources and present in all environments. In contrast, different fungal taxa played different roles in C degradation depending on the soil environment. Overall, our findings reveal that C utilization is driven by similar prokaryotic populations along a glacier forefield, while the distribution of active fungal populations are more influenced by environmental factors.

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Section: Taxa-specific Associations With C Sources and Ssd: Do Soils supporting

confidence: 90%

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields

Rime

Hartmann

Stierli

et al. 2016

Soil Biology and Biochemistry

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“…Kangiella are related to the hydrocarbon degrading Alcanivorax, but no such activity has been associated with Kangiella and no genes for hydrocarbon degradation have been identified. Kangiella has been reported to have the ability to degrade lignocellulose (Darjany et al, 2014 ) as well as algicidal activity (Shi et al, 2013 ), and there were genes annotated as toxins and antitoxins with potential algicidal activity in the SAGs, including the hemolycin tlyC . The Kangiella SAGs encode the peptide transporters dppACDF , the phosphate transporter pstABCS as well as the iron (III) transport protein afuB and the heme exporter ccmABCD .…”

Section: Resultsmentioning

confidence: 99%

Bacterial Succession on Sinking Particles in the Ocean's Interior

2017

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Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio campbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 clade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.

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“…A), indicates that the Flavobacteria were a major group of bacteria that were able to rapidly utilize the lignocellulose. This is consistent with a stable isotope probing study that confirmed flavobacteria are important contributors to lignocellulose cycling in salt marshes (Darjany et al ., ). Even under 5% O 2 a.s., the bacterial community was more abundant in the presence of the lignocellulose extract relative to the control, albeit with weaker statistical significance ( t ‐test: P = 0.05; Fig.…”

Section: Discussionmentioning

confidence: 97%

Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon

Ortega‐Arbulú

Pichler

Vuillemin

et al. 2018

Environmental Microbiology

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Summary Fungi living in sediments (‘mycobenthos’) are hypothesized to play a role in the degradation of organic matter deposited at the land‐sea interface, but the environmental factors influencing the mycobenthos are poorly understood. We used mock community calibrated Illumina sequencing to show that the mycobenthos community structure in a coastal lagoon was significantly changed after exposure to a lignocellulose extract and subsequent development of benthic anoxia over a relatively short (10 h) incubation. Saprotrophic taxa dominated and were selected for under benthic anoxia, specifically Aquamyces (Chytridiomycota) and Orbilia (Ascomycota), implicating these genera as important benthic saprotrophs. Protein encoding genes involved in energy and biomass production from Fungi and the fungal‐analogue group Labyrinthulomycetes had the highest increase in expression with the added organic matter compared with all other groups, indicating that lignocellulose stimulates metabolic activity in the mycobenthos. Flavobacteria dominated the active bacterial community that grew rapidly with the lignocellulose extract and crashed sharply upon O2 depletion. Our findings indicate that the diversity, activity and trophic potential of the mycobenthos changes rapidly in response to organic matter and decreasing O2 concentrations, which together with heterotrophic Flavobacteria, undergo ‘boom and bust’ dynamics during lignocellulose degradation in estuarine ecosystems.

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Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing

Cited by 28 publications

References 76 publications

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields

Bacterial Succession on Sinking Particles in the Ocean's Interior

Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon

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