scholarly journals Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11836
Author(s):  
Fumiaki Mori ◽  
Yu Umezawa ◽  
Ryuji Kondo ◽  
Gregory N. Nishihara ◽  
Minoru Wada
Keyword(s):  
Oxygen Consumption ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sediment Surface ◽  
Tetrazolium Chloride ◽  
Sediment Samples ◽  
Relative Contribution ◽  
Before And After ◽  
Seasonal Hypoxia ◽  
Potential Oxygen

The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a sharp increase in the relative abundance of sulfate reducing bacteria toward hypoxia. In addition, a notable shift in other bacterial compositions was observed before and after the INT assay incubation. It was Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, that increased markedly during the assay period in the summer samples. These findings have implications not only for members of Delta- and Gammaproteobacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

Potential Oxygen Consumption and Community Composition of Sediment Bacteria in a Seasonally Hypoxic Enclosed Bay

2021 ◽  
Author(s):  
Fumiaki Mori ◽  
Yu Umezawa ◽  
Ruji Kondo ◽  
Gregory N. Nishihara ◽  
Minoru Wada
Keyword(s):  
Oxygen Consumption ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sediment Surface ◽  
Tetrazolium Chloride ◽  
Sediment Samples ◽  
Potential Oxygen

Abstract The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a notable shift in the bacterial community composition before and after the INT assay incubation. Within the bacterial community that was predominated by the ASVs closely related to Woeseia (Woeseiaceae, Gammaproteobacteria), the relative abundance of ASVs affiliated with Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, increased markedly in the summer samples. These findings have implications not only for the group of bacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

Phylogenetic Differentiation of Two Closely RelatedNitrosomonas spp. That Inhabit Different Sediment Environments in an Oligotrophic Freshwater Lake

1999 ◽  
Vol 65 (11) ◽  
pp. 4855-4862 ◽  
Author(s):  
Corinne B. Whitby ◽  
Jon R. Saunders ◽  
Juana Rodriguez ◽  
Roger W. Pickup ◽  
Alan McCarthy
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Freshwater Lake ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Relative Distribution ◽  
Sediment Samples ◽  
Oligonucleotide Hybridization

ABSTRACT The population of ammonia-oxidizing bacteria in a temperate oligotrophic freshwater lake was analyzed by recovering 16S ribosomal DNA (rDNA) from lakewater and sediment samples taken throughout a seasonal cycle. Nitrosospira and Nitrosomonas16S rRNA genes were amplified in a nested PCR, and the identity of the products was confirmed by oligonucleotide hybridization.Nitrosospira DNA was readily identified in all samples, and nitrosomonad DNA of the Nitrosomonas europaea-Nitrosomonas eutropha lineage was also directly detected, but during the summer months only. Phylogenetic delineation with partial (345 bp) 16S rRNA gene sequences of clones obtained from sediments confirmed the fidelity of the amplified nitrosomonad DNA and identified two sequence clusters closely related to either N. europaea or N. eutropha that were equated with the littoral and profundal sediment sites, respectively. Determination of 701-bp sequences for 16S rDNA clones representing each cluster confirmed this delineation. A PCR-restriction fragment length polymorphism (RFLP) system was developed that enabled identification of clones containing N. europaea and N. eutropha 16S rDNA sequences, including subclasses therein. It proved possible to analyze 16S rDNA amplified directly from sediment samples to determine the relative abundance of each species compared with that of the other. N. europaea and N. eutropha are very closely related, and direct evidence for their presence in lake systems is limited. The correlation of each species with a distinct spatial location in sediment is an unusual example of niche adaptation by two genotypically similar bacteria. Their occurrence and relative distribution can now be routinely monitored in relation to environmental variation by the application of PCR-RFLP analysis.

scholarly journals Changes in Active Bacterial Communities before and after Dredging of Highly Polluted Baltic Sea Sediments

2006 ◽  
Vol 72 (10) ◽  
pp. 6800-6807 ◽  
Author(s):  
Anna Edlund ◽  
Janet K. Jansson
Keyword(s):  
Baltic Sea ◽  
Fragment Length Polymorphism ◽  
Polyaromatic Hydrocarbons ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cloning And Sequencing ◽  
Marine Food Web ◽  
Molecular Approaches ◽  
Before And After ◽  
Marine Food

ABSTRACT Bacteria residing in sediments have key functions in the marine food web. However, it has been difficult to correlate the identity and activity of bacteria in sediments due to lack of appropriate methods beyond cultivation-based techniques. Our aim was to use a combination of molecular approaches, bromodeoxyuridine incorporation and immunocapture, terminal restriction fragment length polymorphism, and cloning and sequencing of 16S rRNA genes to assess the composition of growing bacteria in Baltic Sea sediments. The study site was a highly polluted area off the Swedish coast. The sediments were sampled in two consecutive years, before and after remediation, by dredging of the top sediments. Levels of polyaromatic hydrocarbons (PAHs), mercury, and polychlorinated biphenyls were dramatically reduced as a result of the cleanup project. The compositions of growing members of the communities were significantly different at the two sampling periods. In particular, members from the class Deltaproteobacteria and genus Spirochaeta were more dominant before dredging, but members of the classes Gammaproteobacteria and the Flavobacteria represented the most dominant growing populations after dredging. We also cultivated isolates from the polluted sediments that could transform the model PAH compound, phenanthrene. Some of these isolates were confirmed as dominant growing populations by the molecular methods as well. This suite of methods enabled us to link the identity and activity of the members of the sediment communities.

scholarly journals Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay

2019 ◽  
Author(s):  
Caitlin Petro ◽  
Birthe Zäncker ◽  
Piotr Starnawski ◽  
Lara M. Jochum ◽  
Timothy G. Ferdelman ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Direct Evidence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Microbial Populations ◽  
Sediment Surface ◽  
Deep Biosphere ◽  
Near Surface ◽  
Sulfate Reducing ◽  
Core Set

AbstractAnalyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (dsrBgene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g. Chloroflexi & Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.

scholarly journals Microbiome succession during ammonification in eelgrass bed sediments

2017 ◽  
Author(s):  
Cassandra L Ettinger ◽  
Susan L Williams ◽  
Jessica M Abbott ◽  
John J Stachowicz ◽  
Jonathan A Eisen
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ecosystem Functions ◽  
Sediment Samples ◽  
Functional Studies ◽  
Elemental Cycling

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA. Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis. Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates. Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).

scholarly journals Microbiome succession during ammonification in eelgrass bed sediments

2017 ◽  
Author(s):  
Cassandra L Ettinger ◽  
Susan L Williams ◽  
Jessica M Abbott ◽  
John J Stachowicz ◽  
Jonathan A Eisen
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ecosystem Functions ◽  
Sediment Samples ◽  
Functional Studies ◽  
Elemental Cycling

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA. Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis. Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates. Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).

scholarly journals Molecular Biological Detection and Quantification of Novel Fibrobacter Populations in Freshwater Lakes

2009 ◽  
Vol 75 (15) ◽  
pp. 5148-5152 ◽  
Author(s):  
James E. McDonald ◽  
Alexandre B. de Menezes ◽  
Heather E. Allison ◽  
Alan J. McCarthy
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Relative Abundance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sediment Surface ◽  
Rrna Gene ◽  
Freshwater Lakes ◽  
Lake Ecosystems ◽  
The 16S Rrna Gene

ABSTRACT PCR and quantitative PCR (qPCR) primers targeting the 16S rRNA gene were used to detect and quantify members of the genus Fibrobacter in lake water, sediment and colonized cotton taken from two freshwater lakes. Phylogenetic analysis identified two groups of sequences; those clustered with Fibrobacter succinogenes, the type species, and a defined cluster of clones loosely associated with several Fibrobacter sequences observed previously in clone libraries from freshwater environments. 16S rRNA gene sequences recovered in the same way from soil samples and ovine feces in the surrounding land were all F. succinogenes and did not include any from this group of the “freshwater” Fibrobacteres. In all cases, nested PCR was required to detect Fibrobacter 16S rRNA genes, and qPCR analysis of reverse transcribed bacterial community RNA confirmed their very low relative abundance on colonized cotton baits in the water column (at 0, 3, 7, 11, and 13 m) and on the sediment surface (<0.02% of total bacterial rRNA). However, in Esthwaite Water sediment itself, the relative abundance of fibrobacters was 2 orders of magnitude higher (ca. 1% of total bacterial rRNA). The presence of fibrobacters, including the cellulolytic rumen species F. succinogenes, on colonized cellulose samples and in lake sediment suggests that these organisms may contribute to the primary degradation of plant and algal biomass in freshwater lake ecosystems.

scholarly journals Cohort Specific Effects of Cereal-bar Supplementation in Overweight Patients With or Without Type 2 Diabetes Mellitus

2016 ◽  
Author(s):  
Chieh Jason Chou ◽  
Chris Lauber ◽  
Anirikh Chakrabarti ◽  
Jay Siddharth ◽  
Anne Chalut-Carpentier ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Alpha Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Community Interactions ◽  
Nutritional Interventions ◽  
Disease States ◽  
Specific Effects ◽  
Before And After

AbstractThe importance of gut microbes to metabolic health is becoming more evident and nutrition-based therapies to alter the composition of bacterial communities to manage metabolic disease are an attractive avenue to ameliorate some effects of Western diets. While the composition of gut microbial communities can vary significantly across disease states, it is not well known if these communities have common responses to nutritional interventions. To better understand fiber-bacterial community interactions, we collected biological parameters and fecal samples of overweight non-diabetic (OND) and diabetic (OD) individuals before and after daily supplementation of 2.8 g β-glucan on their habitual diet for 30 days. Fecal bacterial communities in an age-matched cohort were measured by sequencing partial 16S rRNA genes and imputed metagenomic content. Unexpectedly, we observed disconnected responses of biological measurements and the bacterial community. Based on average effect size, biological measurements were greater in the OND group while effects on the bacterial community were greatest on the OD cohort, and we suspect these observations are due to the significantly lower alpha diversity in the OD cohort. Our data indicate that responses to fiber supplementation are cohort specific and this should be considered when manipulating the microbiome via fiber supplementation.

Sign in / Sign up

Export Citation Format

Share Document