Microbial Community Structure in the Sediments and Its Relation to Environmental Factors in Eutrophicated Sancha Lake

To study the microbial community structure in sediments and its relation to eutrophication environment factors, the sediments and the overlying water of Sancha Lake were collected in the four seasons. MiSeq high-throughput sequencing was conducted for the V3–V4 hypervariable regions of the 16S rRNA gene and was used to analyze the microbial community structure in sediments. Pearson correlation and redundancy analysis (RDA) were conducted to determine the relation between microbial populations and eutrophic factors. The results demonstrated four main patterns: (1) in the 36 samples that were collected, the classification annotation suggested 64 phyla, 259 classes, 476 orders, 759 families, and 9325 OTUs; (2) The diversity indices were ordered according to their values as with summer > winter > autumn > spring; (3) The microbial populations in the four seasons belonged to two distinct characteristic groups; (4) pH, dissolved oxygen (DO), total phosphorus (TP), and total nitrogen (TN) had significant effects on the community composition and structure, which further affected the dissolved total phosphorus (DTP) significantly. The present study demonstrates that the microbial communities in Sancha Lake sediments are highly diverse, their compositions and distributions are significantly different between spring and non-spring, and Actinobacteria and Cyanobacteria may be the key populations or indicator organisms for eutrophication.

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Comparative Analysis of Bacterial and Archaeal Community Structure in Microwave Pretreated Thermophilic and Mesophilic Anaerobic Digesters Utilizing Mixed Sludge under Organic Overloading

Water ◽

10.3390/w12030887 ◽

2020 ◽

Vol 12 (3) ◽

pp. 887 ◽

Cited By ~ 4

Author(s):

Gokce Kor-Bicakci ◽

Emine Ubay-Cokgor ◽

Cigdem Eskicioglu

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Biogas Production ◽

Archaeal Community ◽

Rrna Gene ◽

Anaerobic Digesters ◽

Pretreatment Conditions ◽

The Impact

The effects of microwave (MW) pretreatment were investigated by six anaerobic digesters operated under thermophilic and mesophilic conditions at high organic loading rates (4.9–5.7 g volatile solids/L/d). The experiments and analyses were mainly designed to reveal the impact of MW pretreatment and digester temperatures on the process stability and microbial community structure by correlating the composition of microbial populations with volatile fatty acid (VFA) concentrations. A slight shift from biogas production (with a reasonable methane content) to VFA accumulation was observed in the thermophilic digesters, especially in the MW-irradiated reactors. Microbial population structure was assessed using a high-throughput sequencing of 16S rRNA gene on the MiSeq platform. Microbial community structure was slightly affected by different MW pretreatment conditions, while substantially affected by the digester temperature. The phylum Bacteroidetes proliferated in the MW-irradiated mesophilic digesters by resisting high-temperature MW (at 160 °C). Hydrogenotrophic methanogenesis (mostly the genus of Methanothermobacter) was found to be a key route of methane production in the thermophilic digesters, whereas aceticlastic methanogenesis (mostly the genus of Methanosaeta) was the main pathway in the mesophilic digesters.

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Analysis of Microbial Community Structure and Volatile Compounds in the Pit Mud Used for Manufacturing Taorong-type Baijiu Based on High-Throughput Sequencing

10.21203/rs.3.rs-1097837/v1 ◽

2021 ◽

Author(s):

Yanbo Liu ◽

Mengxiao Sun ◽

Pei Hou ◽

Wenya Wang ◽

Xiangkun Shen ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Qualitative Analysis ◽

Volatile Compounds ◽

High Throughput ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Solid Phase ◽

Gas Chromatography Mass Spectrometry ◽

Pit Mud

Abstract In this study, the pit mud used in manufacturing Taorong-type Baijiu was collected from the upper, middle, lower and bottom layers of pits in Henan Yangshao Liquor Co., LTD. Besides, high-throughput sequencing (HTS) technology was adopted to analyze the microbial community structure of the pit mud. In addition, the volatile compounds in the pit mud were subjected to preliminarily qualitative analysis through headspace-solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS). The results of HTS demonstrated that there were 5, 3, 5 and 5 dominant bacterial phyla (including 11, 11, 9 and 8 dominant bacterial genera) and 3, 3, 3 and 3 dominant fungal phyla (including 4, 7, 7 and 5 dominant fungal genera) in the pit mud from F-S (upper), G-Z (middle), H-X (lower) and I-D (bottom), respectively. The qualitative analysis results of volatile compounds demonstrated that a total of 78 kinds of volatile compounds were detected in the pit mud, including 46, 45, 39 and 49 kinds in the pit mud from F-S, G-Z, H-X and I-D, respectively. Ester and acid were the two main components in the pit mud. Meanwhile, the correlation between microorganisms and main volatile compounds in the pit mud was analyzed. Moreover, Lentimicrobium, Syner-01 and Blvii28_wastewater-sludge group were found for the first time in the pit mud used for manufacturing Taorong-type Baijiu. The findings of this study could provide a theoretical foundation for improving the quality of pit mud and the flavor of Taorong-type Baijiu.

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Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa006 ◽

2020 ◽

Vol 96 (2) ◽

Cited By ~ 4

Author(s):

Kärt Kanger ◽

Nigel G H Guilford ◽

HyunWoo Lee ◽

Camilla L Nesbø ◽

Jaak Truu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Solid State ◽

Food Waste ◽

Microbial Community Structure ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Waste Paper ◽

Rrna Gene ◽

Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

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Defining marine microbial biomes from environmental and dispersal filtered metapopulations

10.1101/141077 ◽

2017 ◽

Author(s):

Markus V. Lindh

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Spatial Scales ◽

Dispersal Limitation ◽

Global Ocean ◽

Microbial Populations ◽

Microbial Biogeography ◽

Metapopulation Theory ◽

Mock Communities

SummaryEnergy and matter fluxes essential for all life1 are modulated by spatial and temporal shifts in microbial community structure resulting from environmental and dispersal filtering2,3, emphasizing the continued need to characterize microbial biogeography4,5. Yet, application of metapopulation theory, traditionally used in general ecology for understanding shifts in biogeographical patterns among macroorganisms, has not been tested extensively for defining marine microbial populations filtered by environmental conditions and dispersal limitation at global ocean scales. Here we show, from applying metapopulation theory on two major global ocean datasets6,7, that microbial populations exhibit core- and satellite distributions with cosmopolitan compared to geographically restricted distributions of populations. We found significant bimodal occupancy-frequency patterns (the different number of species occupying different number of patches) at varying spatial scales, where shifts from bimodal to unimodal patterns indicated environmental and dispersal filtering. Such bimodal occupancy-frequency patterns were validated in Longhurst’s classical biogeographical framework and in silico where observed bimodal patterns often aligned with specific biomes and provinces described by Longhurst and where found to be non-random in randomized datasets and mock communities. Taken together, our results show that application of metapopulation theory provides a framework for determining distinct microbial biomes maintained by environmental and dispersal filtering.

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Assessment of microbial communities in Nakivubo wetland and its catchment areas in Lake Victoria Basin, Uganda

10.1101/2020.12.08.413922 ◽

2020 ◽

Author(s):

Bernard N. Kanoi ◽

Maribet Gamboa ◽

Doris Ngonzi ◽

Thomas G. Egwang

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Diversity ◽

Microbial Community Structure ◽

Lake Victoria ◽

Rrna Gene ◽

Lake Victoria Basin ◽

Structure Changes ◽

Catchment Areas ◽

Polluted Sites

AbstractMicrobial community structure changes are key in detecting and characterizing the impacts of anthropogenic activities on aquatic ecosystems. Here, we evaluated the effect of river pollution of industrial and urban sites on the microbial community composition and distribution in the Nakivubo wetland and its catchment areas in Lake Victoria basin, Uganda. Samples were collected from two industrial and one urban polluted sites and the microbial diversity was analyzed based on a 16S rRNA gene clone library. Differences in microbial diversity and community structure were observed at different sampling points. Bacteria associated with bioremediation were found in sites receiving industrial waste, while a low proportion of important human-pathogenic bacteria were seen in urban polluted sites. While Escherichia spp. was the most dominant genus of bacteria for all sites, three unique bacteria, Bacillus sp., Pseudomonas sp., Thermomonas sp., which have been reported to transform contaminants such as heavy metals and hydrocarbons (such as oils) by their metabolic pathways were also identified. Our results may serve as a basis for further studies assessing microbial community structure changes among polluted sites at Nakivubo Water Channel for management and monitoring. The diversity of natural microbial consortia could also be a rich bioprospecting resource for novel industrial enzymes, medicinal and bioactive compounds.

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Natural Attenuation of Mn(II) in Metal Refinery Wastewater: Microbial Community Structure Analysis and Isolation of a New Mn(II)-Oxidizing Bacterium Pseudomonas sp. SK3

Water ◽

10.3390/w11030507 ◽

2019 ◽

Vol 11 (3) ◽

pp. 507 ◽

Cited By ~ 3

Author(s):

Santisak Kitjanukit ◽

Kyohei Takamatsu ◽

Naoko Okibe

Keyword(s):

Community Structure ◽

Microbial Community ◽

Structure Analysis ◽

Microbial Community Structure ◽

Natural Attenuation ◽

Rrna Gene ◽

Pseudomonas Sp ◽

Refinery Wastewater ◽

Pipe Surface

Natural attenuation of Mn(II) was observed inside the metal refinery wastewater pipeline, accompanying dark brown-colored mineralization (mostly MnIVO2 with some MnIII2O3 and Fe2O3) on the inner pipe surface. The Mn-deposit hosted the bacterial community comprised of Hyphomicrobium sp. (22.1%), Magnetospirillum sp. (3.2%), Geobacter sp. (0.3%), Bacillus sp. (0.18%), Pseudomonas sp. (0.03%), and non-metal-metabolizing bacteria (74.2%). Culture enrichment of the Mn-deposit led to the isolation of a new heterotrophic Mn(II)-oxidizer Pseudomonas sp. SK3, with its closest relative Ps. resinovorans (with 98.4% 16S rRNA gene sequence identity), which was previously unknown as an Mn(II)-oxidizer. Oxidation of up to 100 mg/L Mn(II) was readily initiated and completed by isolate SK3, even in the presence of high contents of MgSO4 (a typical solute in metal refinery wastewaters). Additional Cu(II) facilitated Mn(II) oxidation by isolate SK3 (implying the involvement of multicopper oxidase enzyme), allowing a 2-fold greater Mn removal rate, compared to the well-studied Mn(II)-oxidizer Ps. putida MnB1. Poorly crystalline biogenic birnessite was formed by isolate SK3 via one-electron transfer oxidation, gradually raising the Mn AOS (average oxidation state) to 3.80 in 72 h. Together with its efficient in vitro Mn(II) oxidation behavior, a high Mn AOS level of 3.75 was observed with the pipeline Mn-deposit sample collected in situ. The overall results, including the microbial community structure analysis of the pipeline sample, suggest that the natural Mn(II) attenuation phenomenon was characterized by robust in situ activity of Mn(II) oxidizers (including strain SK3) for continuous generation of Mn(IV). This likely synergistically facilitated chemical Mn(II)/Mn(IV) synproportionation for effective Mn removal in the complex ecosystem established in this artificial pipeline structure. The potential utility of isolate SK3 is illustrated for further industrial application in metal refinery wastewater treatment processes.

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Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil

International Journal of Molecular Sciences ◽

10.3390/ijms20092265 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2265 ◽

Cited By ~ 9

Author(s):

Liangxiang Dai ◽

Guanchu Zhang ◽

Zipeng Yu ◽

Hong Ding ◽

Yang Xu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Drought Tolerance ◽

Microbial Communities ◽

Microbial Community Structure ◽

Defense Mechanism ◽

Developmental Stages ◽

Rrna Gene ◽

Special Importance ◽

Arachis Hypogaea L

Background: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts. Method: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts. Results: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance. Conclusion: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.

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Dynamic changes in environment condition and microbial community structure in trench and flat seabed sediments of Tokyo Bay, Japan

Water Science & Technology ◽

10.2166/wst.2005.0298 ◽

2005 ◽

Vol 52 (9) ◽

pp. 107-114 ◽

Cited By ~ 1

Author(s):

U. Hasanudin ◽

M. Fujita ◽

Y. Koibuchi ◽

K. Fujie

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Sulfur Cycle ◽

Chemical Environment ◽

Tokyo Bay ◽

Dynamic Changes ◽

Overlying Water ◽

Anoxic Conditions ◽

Seabed Sediments

Dynamic changes in the chemical environment in the bottom of overlying water and microbial community structure in trench and flat seabed sediments were evaluated during summer and autumn in Tokyo Bay, Japan, to elucidate the response of microbial community changes as a consequence of dredging activity. Quinone profile analysis was performed to evaluate the changes in microbial community structure in the sediments. Bottom shape and location of each station affected the chemical environment of the overlying water. The trench bottom shape had longer anoxic conditions than the flat bottom shape. Nitrogen and phosphorus concentrations affected the microbial density in the sediment. During anoxic conditions, the ubiquinone/menaquinone ratio (UQ/MK) was less than unity and increased with rising dissolved oxygen (DO) concentrations. The dominant quinone species in the trench and flat seabed sediments were MK with 6 and 7 isoprene units (MK-6 and MK-7) and UQ with 8 and 9 isoprene units (UQ-8 and UQ-9). MK-6 and UQ-8 containing bacteria might have a great influence on the sulfur cycle of the aquatic ecosystem. While, MK-7 and UQ-9 containing bacteria correlated with the deposition of phototropic bacteria cells onto the seabed sediment. The trench bottom shape contained higher concentrations of MK-6, MK-7, UQ-8 and UQ-9, especially during summer.

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PSIX-6 Dietary crude protein modifies fecal microbial populations independent of feed efficiency status in dairy cows

Journal of Animal Science ◽

10.1093/jas/skab235.787 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 439-440

Author(s):

Alvaro Morales ◽

Leticia Campos ◽

Jacquelyn Prestegaard ◽

Kayla Alward ◽

Connor Owens ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Feed Intake ◽

Feed Efficiency ◽

Crude Protein ◽

High Energy ◽

Repeated Measurements ◽

Rrna Gene ◽

Fecal Microbiome

Abstract Understanding the composition and structure of the fecal microbial community may provide insight into bacterial adaptation to dietary changes in cattle. The aim of this study was to determine relationships among the fecal microbiome, residual feed intake (RFI) and residual net energy intake (REI) with diets varying in crude protein (CP). Four Holstein lactating cows (806 ± 38 kg of BW) were randomly assigned to one of two treatments (LOW: 13.2% and BASE:16.6% CP) in a crossover design (2 periods of 18 d each). Cows were 260 ± 62 days in milk (DIM) and averaged 26.5 ± 12.0 kg milk yield (MY). Diets were formulated to meet animal needs. Individual feed intake measured by a Calan Gate system was used to calculate daily dry matter intake (DMI). BW, MY and milk components were also measured daily. A linear mixed model with repeated measurements over time was used to evaluate diet effect on DMI, MY, RFI and REI in SAS. Individual fecal samples were collected at the end of each period and extracted DNA was subject to 16S rRNA gene deep amplicon sequencing. Operational Taxonomic Units (OTU) were obtained using ≥97% similarity (SILVA database) and microbial community structure was assessed using alpha and beta diversity measures. No significant differences in phenotypic variables evaluated were observed between treatments or periods. We identified 927 concordant OTU among all cows, with 505 novel OTU identified in BASE cows and 403 in LOW cows. Microbial community structure was similar between treatments and feed efficiency measures. One OTU class, Erysipelotrichi, increased in abundance (P = 0.014) in BASE compared to LOW treatment. Findings reflect previous literature in which Erysipelotrichi was associated with high energy or high fat diets. Although no differences were observed in the phenotypic measurements between treatments, metagenomics analyses indicated differences in specific fecal microbial abundance.

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Multistage A-O Activated Sludge Process for Paraformaldehyde Wastewater Treatment and Microbial Community Structure Analysis

Journal of Chemistry ◽

10.1155/2016/2746715 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 6

Author(s):

Danyang Zheng ◽

Yujiao Sun ◽

Huijuan Li ◽

Sidan Lu ◽

Mingjun Shan ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Activated Sludge ◽

Microbial Diversity ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Diversity Index ◽

Public Health Issue ◽

Activated Sludge Process ◽

Degrading Bacteria

In recent years, the effect of formaldehyde on microorganisms and body had become a global public health issue. The multistage combination of anaerobic and aerobic process was adopted to treat paraformaldehyde wastewater. Microbial community structure in different reaction stages was analyzed through high-throughput sequencing. Results showed that multistage A-O activated sludge process positively influenced polyformaldehyde wastewater. The removal rates of formaldehyde were basically stable at more than 99% and those of COD were about 89%. Analysis of the microbial diversity index indicated that the microbial diversity of the reactor was high, and the treatment effect was good. Moreover, microbial community had certain similarity in the same system. Microbial communities in different units also showed typical representative characteristics affected by working conditions and influent concentrations. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant fungal genera in the phylum level of community composition. As to family and genus levels, Peptostreptococcaceae was distributed at various stages and the dominant in this system. This bacterium also played an important role in organic matter removal, particularly decomposition of the acidified middle metabolites. In addition, Rhodobacteraceae and Rhodocyclaceae were the formaldehyde-degrading bacteria found in the reactor.

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