Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

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Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽

10.1128/mbio.00584-12 ◽

2013 ◽

Vol 4 (2) ◽

Cited By ~ 128

Author(s):

Jizhong Zhou ◽

Wenzong Liu ◽

Ye Deng ◽

Yi-Huei Jiang ◽

Kai Xue ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Diversity ◽

Microbial Community Structure ◽

Community Assembly ◽

Ecosystem Functioning ◽

Dominant Role ◽

Microbial Biodiversity ◽

Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

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Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

International Journal of Molecular Sciences ◽

10.3390/ijms20092125 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2125 ◽

Cited By ~ 3

Author(s):

Muhammad Imran Ghani ◽

Ahmad Ali ◽

Muhammad Jawaad Atif ◽

Muhammad Ali ◽

Bakht Amin ◽

...

Keyword(s):

Microbial Community ◽

High Throughput ◽

Soil Microbial Communities ◽

Illumina Miseq ◽

Soil Microbiome ◽

Plant Residues ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Community Structures ◽

Microbial Community Structures

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

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Illumina MiSeq sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates

Chemosphere ◽

10.1016/j.chemosphere.2018.03.025 ◽

2018 ◽

Vol 201 ◽

pp. 578-585 ◽

Cited By ~ 21

Author(s):

Xuehui Xie ◽

Na Liu ◽

Jing Ping ◽

Qingyun Zhang ◽

Xiulin Zheng ◽

...

Keyword(s):

Wastewater Treatment ◽

Microbial Community ◽

Illumina Miseq ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Dyeing Wastewater

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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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Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing

Applied Microbiology and Biotechnology ◽

10.1007/s00253-015-7073-4 ◽

2015 ◽

Vol 100 (3) ◽

pp. 1469-1478 ◽

Cited By ~ 34

Author(s):

Jing You ◽

Gang Wu ◽

Fuping Ren ◽

Qi Chang ◽

Bo Yu ◽

...

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Illumina Miseq ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Microbial Community Dynamics

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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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