Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

Beaudoin, David J.; Carmichael, Catherine A.; Nelson, Robert K.; Reddy, Christopher M.; Teske, Andreas; Edgcomb, Virginia P.

doi:10.1016/j.dsr2.2014.01.007

Cited by 15 publications

(8 citation statements)

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“…In addition to abiotic conditions, biotic interactions can also influence benthic protist communities (i.e., top‐down controls). For example, benthic protists can impose significant grazing effects on bacterial community patterns and further influence hydrocarbon‐degrading processes in marine sediments (Beaudoin et al, ). This kind of driving force contributes to the relative importance of species sorting in protist communities because bacterial communities are also under selective pressure from local environments.…”

Section: Discussionmentioning

confidence: 99%

“…Importantly, protists play diverse roles in maintaining benthic ecosystem functioning. For example, protists exert significant influences on bacterial communities via grazing effects in deep‐sea sediments and further alter the hydrocarbon‐degrading process (Beaudoin et al, ). Metabolically active protists are widely detected in the subsurface of sea floors (Edgcomb, Kysela, Teske, de Vera Gomez, & Sogin, ), in which protists maintain important biogeochemical cycles (Edgcomb et al, ).…”

Section: Introductionmentioning

confidence: 99%

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Protist diversity and community assembly in surface sediments of the South China Sea

Huang

2019

MicrobiologyOpen

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Protists are pivotal components of marine ecosystems in terms of their high diversity, but protist communities have been poorly explored in benthic environments. Here, we investigated protist diversity and community assembly in surface sediments in the South China Sea (SCS) at a basin scale. Pyrosequencing of 18S rDNA was performed for a total of six samples taken from the surface seafloor at water depths ranging from 79 to 2,939 m. We found that Cercozoa was the dominant group, accounting for an average of 39.9% and 25.3% of the reads and operational taxonomic units (OTUs), respectively. The Cercozoa taxa were highly diverse, comprising 14 phylogenetic clades, six of which were affiliated with unknown groups belonging to Filosa and Endomyxa. Fungi were also an important group in both read‐ (18.1% on average) and OTU‐derived (9.3% on average) results. Moreover, the turnover patterns of the protist communities were differently explained by species sorting (53.3%), dispersal limitation (33.3%), mass effects (0%), and drift (13.3%). In summary, our findings show that the basin‐wide protist communities in the surface sediments of the SCS are primarily dominated by Cercozoa and are mainly assembled by species sorting and dispersal limitation.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Protist diversity and community assembly in surface sediments of the South China Sea

Huang

2019

MicrobiologyOpen

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“…Alternatively, we propose they may enter through marine snow or phytoplankton, both of which provides food for zooplankton. Food‐web interactions will influence degradation rates of oil in a multitude of ways, such as bacterivorous protists that graze on the oil‐consuming bacterial community potentially decreasing degradation rates (Beaudoin et al ).…”

Section: Background On the Study Of Marine Snow And Oil Spillsmentioning

confidence: 99%

The role of microbial exopolymers in determining the fate of oil and chemical dispersants in the ocean

Quigg

Passow

Chin

et al. 2016

Limnol Oceanogr Letters

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The production of extracellular polymeric substances (EPS) by planktonic microbes can influence the fate of oil and chemical dispersants in the ocean through emulsification, degradation, dispersion, aggregation, and/or sedimentation. In turn, microbial community structure and function, including the production and character of EPS, is influenced by the concentration and chemical composition of oil and chemical dispersants. For example, the production of marine oil snow and its sedimentation and flocculent accumulation to the seafloor were observed on an expansive scale after the Deepwater Horizon oil spill in the Northern Gulf of Mexico in 2010, but little is known about the underlying control of these processes. Here, we review what we do know about microbially produced EPS, how oil and chemical dispersant can influence the production rate and chemical and physical properties of EPS, and ultimately the fate of oil in the water column. To improve our response to future oil spills, we need a better understanding of the biological and physiochemical controls of EPS production by microbes under a range of environmental conditions, and in this paper, we provide the key knowledge gaps that need to be filled to do so. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Scientific Significance StatementExtracellular polymeric substances (EPS) are a group of chemically heterogeneous polymers released into the environment by microbes (bacteria, archaea, and phytoplankton), often in response to environmental stresses. EPS serve an important role in determining the fate and transport of oil after a spill, but relatively little is known about EPS production in relation to oil and dispersants, especially at molecular and chemical levels. Here, we summarize the scope of our current knowledge and identify major knowledge gaps. 3Limnology and Oceanography Letters 1, 2016, 3-26

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“…Furthermore, some microbes can survive in low energy conditions, such as subsurface sediments (Ciobanu et al 2014) and they may influence the community composition by consuming or outcompeting other microbes. Some common protist taxa consume bacterial and fungal communities in terrestrial soils and marine sediments (Beaudoin et al 2016;Dumack et al 2019Dumack et al , 2020Khanipour Roshan et al 2021), but there is little information about their impact on sedDNA integrity and composition during chilled sediment storage.…”

Section: Introductionmentioning

confidence: 99%

Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies

Brasell¹,

Pochon²,

Howarth³

et al. 2022

MBMG

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Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.

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Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

Cited by 15 publications

References 60 publications

Protist diversity and community assembly in surface sediments of the South China Sea

Protist diversity and community assembly in surface sediments of the South China Sea

The role of microbial exopolymers in determining the fate of oil and chemical dispersants in the ocean

Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies

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Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

Cited by 15 publications

References 60 publications

Protist diversity and community assembly in surface sediments of the South China Sea

Protist diversity and community assembly in surface sediments of the South China Sea

The role of microbial exopolymers in determining the fate of oil and chemical dispersants in the ocean

﻿Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies

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Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies