Seasonal variations and co-occurrence networks of bacterial communities in the water and sediment of artificial habitat in Laoshan Bay, China

Marine bacteria in the seawater and seafloor are essential parts of Earth’s biodiversity, as they are critical participants of the global energy flow and the material cycles. However, their spatial-temporal variations and potential interactions among varied biotopes in artificial habitat are poorly understood. In this study, we profiled the variations of bacterial communities among seasons and areas in the water and sediment of artificial reefs using 16S rRNA gene sequencing, and analyzed the potential interaction patterns among microorganisms. Distinct bacterial community structures in the two biotopes were exhibited. The Shannon diversity and the richness of phyla in the sediment were higher, while the differences among the four seasons were more evident in the water samples. The seasonal variations of bacterial communities in the water were more distinct, while significant variations among four areas were only observed in the sediment. Correlation analysis revealed that nitrite and mud content were the most important factors influencing the abundant OTUs in the water and sediment, respectively. Potential interactions and keystone species were identified based on the three co-occurrence networks. Results showed that the correlations among bacterial communities in the sediment were lower than in the water. Besides, the abundance of the top five abundant species and five keystone species had different changing patterns among four seasons and four areas. These results enriched our understanding of the microbial structures, dynamics, and interactions of microbial communities in artificial habitats, which could provide new insights into planning, constructing and managing these special habitats in the future.

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Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

Biogeosciences Discussions ◽

10.5194/bgd-12-10233-2015 ◽

2015 ◽

Vol 12 (13) ◽

pp. 10233-10269 ◽

Cited By ~ 3

Author(s):

J. Comte ◽

C. Lovejoy ◽

S. Crevecoeur ◽

W. F. Vincent

Keyword(s):

Bacterial Communities ◽

High Throughput Sequencing ◽

Habitat Preferences ◽

Keystone Species ◽

Small World ◽

Rrna Gene ◽

Permafrost Degradation ◽

Bacterial Phyla ◽

Organic Carbon Concentration ◽

Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

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Digestive gland microbiome of Pleurobema cordatum: mesocosms induce dysbiosis

Journal of Molluscan Studies ◽

10.1093/mollus/eyaa024 ◽

2020 ◽

Vol 86 (4) ◽

pp. 280-289

Author(s):

Alison K Aceves ◽

Paul D Johnson ◽

Carla L Atkinson ◽

Brian C van Ee ◽

Stephen A Bullard ◽

...

Keyword(s):

Digestive Gland ◽

Gut Microbiome ◽

Bacterial Communities ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Artificial Rearing ◽

Tennessee River ◽

Wasting Syndrome ◽

Water And Sediment ◽

Rrna Gene Sequencing

ABSTRACT Herein, we characterized the digestive gland (‘gut’) bacterial community (microbiome) of the Ohio pigtoe, Pleurobema cordatum (Rafinesque, 1820), using 16S rRNA gene sequencing. Two populations were compared: wild P. cordatum (n = 5) from the Tennessee River and P. cordatum (n = 9) relocated to artificial mesocosms and exposed to various thermal regimes for 2 weeks. We also characterized the bacterial communities from the habitat (water and sediment) of these wild and mesocosm-held populations. The gut microbiome of wild P. cordatum was dominated by members of the bacterial phylum Tenericutes (72%). By contrast, the gut microbiome of mesocosm-held P. cordatum was dominated by members of the bacterial phylum Proteobacteria (64%). We found no temperature-associated difference in the gut microbiome of mesocosm-held P. cordatum. The bacterial communities of water and sediment from the Tennessee River were diverse and distinct from those of the studied mussels. By contrast, the bacterial communities of water and sediment in the mesocosms were dominated by Proteobacteria. These results suggest that when the studied mussels were moved into artificial rearing environments, their gut microbiome shifted to reflect that of their habitat (i.e. an increase in Proteobacteria). Moreover, the abundance of Tenericutes (also previously reported in other unionids) was reduced from 72% in wild mussels to 3% in mesocosm-held mussels. As a result, we think that mesocosm-held P. cordatum became dysbiotic, which could explain the observed wasting syndrome and associated trickling mortalities in captive P. cordatum.

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206 Characterization of the Rumen Bacterial Communities of Grass-fed and Grain-fed Bison Heifers

Journal of Animal Science ◽

10.1093/jas/skaa278.300 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 164-164

Author(s):

Anlly M Fresno Rueda ◽

Jason Griffin ◽

Carter Kruse ◽

Benoit St-Pierre

Keyword(s):

North American ◽

Bacterial Communities ◽

Sequence Data ◽

Rumen Fluid ◽

Illumina Miseq ◽

Rank Test ◽

Rrna Gene ◽

The North ◽

Abundant Otus ◽

Blue Creek

Abstract The ruminal bacterial environment of the North American bison has remained largely unexplored. The current study aimed to compare the diversity and composition of ruminal bacteria between bison heifers on two different diets. Stomach tubing was used to collect rumen fluid from lifetime grass-fed heifers between 27 and 30 months of age distributed between 2 ranches located in Standing-Butte (n = 17), SD, and Blue-Creek (n = 17), NE, respectively. A second set of samples was collected after the same individuals had been transitioned to a grain-based diet for 100 days. Bacterial composition was determined by Illumina MiSeq (2×300) sequencing of PCR amplicons generated from the V1-V3 region of the 16S rRNA gene. Next-Generation Sequence data was analyzed using a combination of custom Perl scripts, and publicly available software (Mothur v.1.40, RDP classifier and NCBI Blast). Taxonomic analysis identified Bacteroidetes and Firmicutes as the dominant phyla across all samples analyzed. A total of 61,746 and 68,437 species-level Operational Taxonomic Units (OTUs) were identified in grass-fed heifers, in contrast to 15,003 and 23,458 OTUs that were found in the same animals on a grain-based diet. A comparative analysis using the most abundant OTUs from each group was conducted using the Kruskal-Wallis sum-rank test. In the Standing Butte heifers, 24 abundant OTUs were found to be different between diets (P < 0.05), including BP_31-10446 (µ grass = 0.3% vs µ grain = 3.2%) and BP_25-00404 (µ grass = 0.4% vs µ grain = 4.1%). In the Blue Creek heifers, 20 of the most abundant OTUs were found to be different between diets (P < 0.05), including BP_18-00869 (µ grass = 1.4% vs µ grain = 0.4%) and BCRC_1-00422 (µ grass = 0.07% vs µ grain = 4.4%). Together, these results indicate that the rumen of the North American bison harbors highly diverse bacterial communities that undergo dramatic changes in response to changes in diet.

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Water and Sediment Bacterial Communities in a Small Mediterranean, Oxygen-Stratified, Saline Lake (Lake Alboraj, SE Spain)

Applied Sciences ◽

10.3390/app11146309 ◽

2021 ◽

Vol 11 (14) ◽

pp. 6309

Author(s):

Yolanda Espín ◽

Alfonso Menchén ◽

José Luis Moreno ◽

David Sanz ◽

Manuel Álvarez-Ortí ◽

...

Keyword(s):

Water Column ◽

Bacterial Communities ◽

Ecological Status ◽

Natura 2000 ◽

Rrna Gene ◽

Natura 2000 Network ◽

Se Spain ◽

Water And Sediment ◽

Different Depths ◽

Physical And Chemical

Lake Alboraj, located in southeast Spain, was declared natural Microreserve and included into European Natura-2000 Network due to its contribution to environmental heritage. Unfortunately, the ecological status of the lake has changed dramatically, mainly due to the lowering of water table caused by groundwater abstractions for irrigation. It is a permanent small karstic lake whose surface has reduced in the last decades to nearly the third part of its historical water level. The water column shows a marked seasonal oxycline, that splits an aerobic upper layer (epilimnion) from an anaerobic layer below (hypolimnion). Sequencing 16S rRNA gene amplicons and applying chemical tools at epilimnion, hypolimnion and sediment, showed a clear gradient in the bacterial community structure, which support the co-existence of assimilatory and dissimilatory microbial mediated reactions. Results allows to infer that microbial stratification could provide various physical and chemical environments at different depths in the water column related to biogeochemical reactions providing N-S-C- recycling processes.

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Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau

10.1101/753616 ◽

2019 ◽

Author(s):

Luciano Lopes Queiroz ◽

Amanda Gonçalves Bendia ◽

Rubens Tadeu Delgado Duarte ◽

Diego Assis das Graças ◽

Artur Luiz da Costa da Silva ◽

...

Keyword(s):

Deep Sea ◽

Bacterial Communities ◽

Sao Paulo ◽

Rrna Gene ◽

São Paulo ◽

Operational Taxonomic Units ◽

Uncultured Bacteria ◽

Abundant Otus ◽

Sediment Layers ◽

Next Generation Sequencing Ngs

AbstractHere we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing (NGS) method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2,456-2,728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaprotebacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

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Seasonal Variations of 2,4-D in Buckhorn Lake

Water Quality Research Journal ◽

10.2166/wqrj.1985.009 ◽

1985 ◽

Vol 20 (1) ◽

pp. 106-117 ◽

Cited By ~ 2

Author(s):

E. Nagy ◽

D.S. Painter

Keyword(s):

Lake Water ◽

Seasonal Variations ◽

Water And Sediment ◽

Streamflow Data ◽

Land Runoff

Abstract A five month survey of 2,4-D in Buckhorn Lake water and sediment, combined with streamflow data, produced estimates of the chemical in the lake. The peak concentrations in the water alone were significantly higher than the documented uses would permit. Two distinct concentration peaks were shown by the chemical: one during the June milfoil control season, and one in late August, indicating a release of 2,4-D from the collapsed and decaying milfoil beds. The observed rates of disappearance of the chemical agreed with reported values, showing a limited persistence in the lake. The presence of 2,4-D in the spring sediments was attributed to land runoff.

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The capacity of wastewater treatment plants drives bacterial community structure and its assembly

Scientific Reports ◽

10.1038/s41598-019-50952-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Young Kyung Kim ◽

Keunje Yoo ◽

Min Sung Kim ◽

Il Han ◽

Minjoo Lee ◽

...

Keyword(s):

Wastewater Treatment ◽

Community Structure ◽

Bacterial Community ◽

Activated Sludge ◽

Community Assembly ◽

Bacterial Communities ◽

Wastewater Treatment Plants ◽

High Capacity ◽

Operating Conditions ◽

Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

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A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽

10.3390/ani11061658 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1658

Author(s):

Jan C. Plaizier ◽

Anne-Mette Danscher ◽

Paula A. Azevedo ◽

Hooman Derakhshani ◽

Pia H. Andersen ◽

...

Keyword(s):

Digestive Tract ◽

Relative Abundance ◽

Bacterial Communities ◽

Dry Matter ◽

Control Diet ◽

Rrna Gene ◽

Ruminal Acidosis ◽

Clustering Patterns ◽

The 16S Rrna Gene ◽

Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

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Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽

10.1016/j.lwt.2021.111579 ◽

2021 ◽

Vol 147 ◽

pp. 111579

Author(s):

Creciana M. Endres ◽

Ícaro Maia S. Castro ◽

Laura D. Trevisol ◽

Juliana M. Severo ◽

Michele B. Mann ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Molecular Characterization ◽

Bacterial Communities ◽

Rrna Gene

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Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽

10.1186/s13568-020-01119-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Shenzheng Zeng ◽

Sukontorn Khoruamkid ◽

Warinphorn Kongpakdee ◽

Dongdong Wei ◽

Lingfei Yu ◽

...

Keyword(s):

Microbial Communities ◽

Well Being ◽

Pacific White Shrimp ◽

Shrimp Farming ◽

Rrna Gene ◽

Microbial Composition ◽

Shrimp Culture ◽

Water And Sediment ◽

Surrounding Environment ◽

Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

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