Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

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High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

10.21203/rs.3.rs-34433/v1 ◽

2020 ◽

Author(s):

Wu Qu ◽

Boliang Gao ◽

Jie Wu ◽

Min Jin ◽

Jianxin Wang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Fungal Community ◽

Amplicon Sequencing ◽

Biotic Factors ◽

Community Structures ◽

Mangrove Sediments ◽

Element Cycling ◽

Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake

10.1101/244657 ◽

2018 ◽

Author(s):

Maozhen Han ◽

Melissa Dsouza ◽

Chunyu Zhou ◽

Hongjun Li ◽

Junqian Zhang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Physicochemical Properties ◽

Microbial Communities ◽

Microbial Ecology ◽

Agricultural Pollution ◽

Agricultural Activities ◽

Sediment Samples ◽

Water And Sediment ◽

Honghu Lake

AbstractBackgroundAgricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear.MethodsWe performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities.ResultsPhysicochemical properties including TN, TP, NO3--N, and NO2--N were correlated with microbial compositional differences in water samples. Likewise, in sediment samples, Sed-OM and Sed-TN correlated with microbial diversity. Oxytetracycline and tetracycline concentration described the majority of the variance in taxonomic and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Finally, the structure of microbial co-associations was influenced by the eutrophication and antibiotic pollution.ConclusionThese analyses of the composition and structure of water and sediment microbial communities in anthropologically-impacted lakes are imperative for effective environmental pollution monitoring. Likewise, the exploration of the associations between environmental variables (e.g. physicochemical properties, and antibiotics) and community structure is important in the assessment of lake water quality and its ability to sustain agriculture. These results show agricultural practices can negatively influence not only the physicochemical properties, but also the biodiversity of microbial communities associated with the Honghu lake ecosystem. And these results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu lake.

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Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato

Microorganisms ◽

10.3390/microorganisms8060834 ◽

2020 ◽

Vol 8 (6) ◽

pp. 834

Author(s):

Naihui Li ◽

Danmei Gao ◽

Xingang Zhou ◽

Shaocan Chen ◽

Chunxia Li ◽

...

Keyword(s):

Community Structure ◽

Organic Carbon ◽

Bacterial Community ◽

Soil Organic Carbon ◽

Microbial Communities ◽

Fungal Community ◽

Soil Microbial Communities ◽

Tomato Seedling ◽

Soil Microbial ◽

Potato Onion

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

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Plumage iridescence is associated with distinct feather microbiota in a tropical passerine

Scientific Reports ◽

10.1038/s41598-019-49220-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Veronika Gvoždíková Javůrková ◽

Erik D. Enbody ◽

Jakub Kreisinger ◽

Kryštof Chmel ◽

Jakub Mrázek ◽

...

Keyword(s):

Sexual Selection ◽

Community Structure ◽

Microbial Communities ◽

Plumage Coloration ◽

Microbial Load ◽

Sexual Dichromatism ◽

Physiological Processes ◽

Fitness Consequences ◽

Future Work

Abstract Birds present a stunning diversity of plumage colors that have long fascinated evolutionary ecologists. Although plumage coloration is often linked to sexual selection, it may impact a number of physiological processes, including microbial resistance. At present, the degree to which differences between pigment-based vs. structural plumage coloration may affect the feather microbiota remains unanswered. Using quantitative PCR and DGGE profiling, we investigated feather microbial load, diversity and community structure among two allopatric subspecies of White-shouldered Fairywren, Malurus alboscapulatus that vary in expression of melanin-based vs. structural plumage coloration. We found that microbial load tended to be lower and feather microbial diversity was significantly higher in the plumage of black iridescent males, compared to black matte females and brown individuals. Moreover, black iridescent males had distinct feather microbial communities compared to black matte females and brown individuals. We suggest that distinctive nanostructure properties of iridescent male feathers or different investment in preening influence feather microbiota community composition and load. This study is the first to point to structural plumage coloration as a factor that may significantly regulate feather microbiota. Future work might explore fitness consequences and the role of microorganisms in the evolution of avian sexual dichromatism, with particular reference to iridescence.

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A quantitative comparison of microbial community structure of estuarine sediments from microcosms and the field

Canadian Journal of Microbiology ◽

10.1139/m86-063 ◽

1986 ◽

Vol 32 (4) ◽

pp. 319-325 ◽

Cited By ~ 19

Author(s):

Thomas W. Federle ◽

Robert J. Livingston ◽

Loretta E. Wolfe ◽

David C. White

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Structure ◽

Ecological Factors ◽

Estuarine Sediments ◽

Physical Factors ◽

Multivariate Statistical ◽

Apalachicola Bay ◽

Sound Experiment

Estuarine soft-bottom sediments in microcosms and the field were compared with regard to microbial community structure. Community structure was determined by analyzing the fatty acids derived from the microbial lipids in the sediments. Fatty acid profiles were compared using a multivariate statistical approach. Experiments were performed using sediments from St. George Sound and Apalachicola Bay, Florida. The community structure of St. George Sound sediments was apparently controlled by epibenthic predators. In Apalachicola Bay, the dominant influences were physical factors related to the flow of the Apalachicola River. In the St. George Sound experiment, microbial communities in the microcosms differed from those in the field after only 2 weeks, and the degree of this difference increased substantially as time progressed. In the Apalachicola Bay experiment, although microbial communities in the microcosms were detectably different from those in the field, the degree of this difference was not large nor did it increase with time. This differential behavior of sediment communities from different sites may be related to the different ecological factors regulating community composition at these sites.

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Linking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter

mBio ◽

10.1128/mbio.01607-19 ◽

2019 ◽

Vol 10 (4) ◽

Cited By ~ 7

Author(s):

Kristin M. Rath ◽

Arpita Maheshwari ◽

Johannes Rousk

Keyword(s):

Community Structure ◽

Microbial Community ◽

Salt Tolerance ◽

Microbial Communities ◽

Bacterial Growth ◽

Soil Microbes ◽

Fungal Growth ◽

Environmental Filter ◽

Trait Distribution ◽

Nonsaline Soil

ABSTRACT The structure and function of microbial communities vary along environmental gradients; however, interlinking the two has been challenging. In this study, salinity was used as an environmental filter to study how it could shape trait distributions, community structures, and the resulting functions of soil microbes. The environmental filter was applied by salinizing nonsaline soil (0 to 22 mg NaCl g−1). Our targeted community trait distribution (salt tolerance) was determined with dose-response relationships between bacterial growth and salinity. The bacterial community structure responses were resolved with Illumina 16S rRNA gene amplicon sequencing, and the microbial functions determined were respiration and bacterial and fungal growth. Salt exposure quickly resulted in filtered trait distributions, and stronger filters resulted in larger shifts. The filtered trait distributions correlated well with community composition differences, suggesting that trait distribution shifts were driven at least partly by species turnover. While salt exposure decreased respiration, microbial growth responses appeared to be characterized by competitive interactions. Fungal growth was highest when bacterial growth was inhibited by the highest salinity, and it was lowest when the bacterial growth rate peaked at intermediate salt levels. These findings corroborated a higher potential for fungal salt tolerance than bacterial salt tolerance for communities derived from a nonsaline soil. In conclusion, by using salt as an environmental filter, we could interlink the targeted trait distribution with both the community structure and resulting functions of soil microbes. IMPORTANCE Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community composition and structure. Here, we apply a conceptual framework to determine how microbial communities influence ecosystem processes, by applying a “top-down” trait-based approach. By determining the dependence of microbial processes on environmental factors (e.g., the tolerance to salinity), we can define the aggregate response trait distribution of the community, which then can be linked to the community structure and the resulting function performed by the microbial community.

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Microbial community structure in the western tropical South Pacific

Biogeosciences ◽

10.5194/bg-15-3909-2018 ◽

2018 ◽

Vol 15 (12) ◽

pp. 3909-3925 ◽

Cited By ~ 8

Author(s):

Nicholas Bock ◽

France Van Wambeke ◽

Moïra Dion ◽

Solange Duhamel

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Structure ◽

N2 Fixation ◽

Phytoplankton Biomass ◽

South Pacific ◽

Global Ocean ◽

Bottom Up

Abstract. Oligotrophic regions play a central role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the western tropical South Pacific (WTSP) remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g., nutrients and light availability) as well as statistical analyses, we estimated the role of bottom–up and top–down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a “typical tropical structure”, characterized by a shallow mixed layer, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Prochlorococcus was especially abundant along the transect, accounting for 68 ± 10.6 % of depth-integrated phytoplankton biomass. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to 26 ± 11.6 % of depth-integrated phytoplankton biomass, while Synechococcus accounted for only 6 ± 6.9 %. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N2 fixation rates and plankton abundances demonstrate the central role of N2 fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom–up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).

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Community structure of micro- and macroflocs in pin-point sludge and the influence of sludge age and potassium addition on microfloc formation

Water Science & Technology ◽

10.2166/wst.2002.0508 ◽

2002 ◽

Vol 46 (1-2) ◽

pp. 405-412 ◽

Cited By ~ 9

Author(s):

E. Müller ◽

K. Kriebitzsch ◽

P.A. Wilderer ◽

S. Wuertz

Keyword(s):

Community Structure ◽

Microbial Communities ◽

Extracellular Polymeric Substances ◽

Point Of View ◽

Sludge Formation ◽

Industrial Plants ◽

Noticeable Improvement ◽

Lower Protein ◽

Utilization Patterns ◽

The Impact

Settling problems caused by pin-point sludge constitute a serious problem in biological wastewater treatment, particularly in many industrial plants. Until now, most studies focused on the relationship between pin-point sludge formation and either shearing forces or the impact of toxicants. This study deals with the community structure in both the micro- and macrofloc fraction which was analyzed by fluorescent in situ hybridization (FISH) and BIOLOG substrate utilization patterns. It was shown that each fraction consisted of different microbial communities with unique metabolic profiles suggesting that pin-point sludge formation is not due to dispersal of intact flocs but to microcolonies growing separately. Alternatively, macroflocs may have an architecture leading to segregation of microbial communities after floc dispersal. Further it could be shown that the formation of microflocs was influenced by sludge age. The best sludge sedimentation was obtained for a sludge age of 5 and 10 days. Additional analysis of extracellular polymeric substances (EPS) suggested that the lower protein to carbohydrate ratio of 10-day-old sludge led to better flocculation compared to 20-day-old sludge containing similar total amounts of EPS. From a practical point of view, addition of potassium (0.1 g/l) effected a noticeable improvement of sludge settleability.

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Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

Applied and Environmental Microbiology ◽

10.1128/aem.00210-17 ◽

2017 ◽

Vol 83 (11) ◽

Cited By ~ 22

Author(s):

Ryan A. Blaustein ◽

Graciela L. Lorca ◽

Julie L. Meyer ◽

Claudio F. Gonzalez ◽

Max Teplitski

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Illumina Sequencing ◽

Symptom Severity ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

The Core ◽

Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

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