scholarly journals Metagenomic analysis of microbial communities in the sediments of a semi-intensive penaeid shrimp culture system

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
M. S. Chithira ◽  
P. V. Aishwarya ◽  
Anjali S. Mohan ◽  
Swapna P. Antony
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Sediment Sample ◽  
Culture System ◽  
High Throughput Sequencing ◽  
Control Strategies ◽  
Penaeid Shrimp ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Shrimp Culture

AbstractThe present study reports metagenomic sequencing and microbial diversity analysis of the sediment samples of a semi-intensive penaeid shrimp culture system. 16S rRNA gene-based high-throughput sequencing revealed distinct and diverse microbial communities in the analyzed sample. Analysis of the results showed a high abundance of Proteobacteria followed by Verrucomicrobia, Bacteroidetes, Planctomycetes, Firmicutes, Cyanobacteria, and Actinobacteria in the metagenome retrieved from the sediment sample. Unclassified bacteria also contributed a significant portion of the metagenome. Two potential shrimp pathogens viz Vibrio harveyi and Acinetobacter lwoffii detected in the sediment sample show the risk associated with the pond. Microbes that play essential roles in nutrient cycling and mineralization of organic compounds such as Bacteroidetes, Planctomycetes, Gammaproteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria could also be identified. The present study provides preliminary data with respect to the microbial community present in the sediments of a shrimp culture system and emphasizes the application of metagenomics in exploring the microbial diversity of aquaculture systems, which might help in the early detection of pathogens within the system and helps to develop pathogen control strategies in semi-intensive aquaculture systems.

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

AMB Express ◽  
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.

scholarly journals Long-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goods

2020 ◽  
Author(s):  
Gina R. Lewin ◽  
Nicole M. Davis ◽  
Bradon R. McDonald ◽  
Adam J. Book ◽  
Marc G. Chevrette ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Species Interactions ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Soluble Sugars ◽  
Mutual Exclusion ◽  
Breakdown Product ◽  
Rrna Gene ◽  
Refuse Dumps

AbstractThe complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months), cellulolytic ability increased then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic and variably cellulolytic enrichment lines. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all the communities, with the mutual exclusion of specific cellulolytic taxa within individual enrichment lines and the high expression of genes associated with the production of antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities.ImportanceMicrobial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut.However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.

scholarly journals Putative functions and co-occurrence patterns of the microbial communities in natural and engineered ecosystems

2021 ◽  
Author(s):  
Yu Xia ◽  
Na Li ◽  
Yiyun Chen ◽  
Weijia Li ◽  
Xuwen He ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Rrna Gene ◽  
Natural Environments ◽  
Anaerobic Digesters ◽  
Network Analyses ◽  
Wb Network ◽  
Almost All ◽  
Occurrence Patterns

Abstract Understanding functions and co-occurrence patterns of microbial communities in various ecosystems enriches the knowledge on ecosystem characteristics and microbial ecology. However, such analyses have rarely been reported. Herein, functions and inter-taxa correlations of microbial communities in a set of natural environments (farmland (SA), forest soil (SB) and Caspian Sea sediments (CSS)) and engineered ecosystems (wastewater treatment plants (FW, WA and WB) and anaerobic digesters (AD)) were studied based on FAPROTAX and network analyses, respectively, by a collection of 115 samples from seven published 16S rRNA gene datasets generated by high-throughput sequencing. The results show that chemoheterotrophy related populations were the most abundant in almost all the communities. Their relative abundances (RAs) in the AD systems were the highest (43.7%±4.2%), followed by those of the soil environments (40.2%±1.9% in SA and 36.4%±2.0% in SB). For each ecosystem, the indicative community and overall community showed differentiations in several function categories. For example, the SA and SB indicative communities showed higher RAs in aerobic chemoheterotrophy, the CSS indicative community showed higher RAs in sulfate respiration, the AD indicative community showed higher RAs in fermentation, and the WB indicative community included higher RAs of predatory/exoparasitic bacteria. Three molecular ecological networks of the communities from the AD, WB and SB datasets were constructed, respectively. The WB network showed the highest proportion of negative correlations (70.4%), possibly attributed to the environmental pressure which aggravated microbial competition. The positively correlated taxa showed lower phylogenetic distances than the negatively correlated taxa on average in each network.

scholarly journals High Diversity in Iron Cycling Microbial Communities in Acidic, Iron-Rich Water of the Pyhäsalmi Mine, Finland

Geofluids ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Malin Bomberg ◽  
Jarno Mäkinen ◽  
Marja Salo ◽  
Päivi Kinnunen
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Mine Water ◽  
Ferrous Iron ◽  
Great Part ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Iron Oxidizers

Microbial communities of iron-rich water in the Pyhäsalmi mine, Finland, were investigated with high-throughput amplicon sequencing and qPCR targeting bacteria, archaea, and fungi. In addition, the abundance ofLeptospirillumandAcidithiobacilluswas assessed with genus-specific qPCR assays, and enrichment cultures targeting aerobic ferrous iron oxidizers and ferric iron reducers were established. The acidic (pH 1.4–2.3) mine water collected from 240 m, 500 m, and 600 m depth from within the mine had a high microbial diversity consisting of 63-114 bacterial, 10-13 archaeal, and 104-117 fungal genera. The most abundant microorganisms in the mine water were typical acid mine drainage (AMD) taxa, such as acidophilic, iron-oxidizingLeptospirillum,Acidiphilum,Acidithiobacillus,Ferrovum, andThermoplasma. The fungi belonged mostly to the phylum Ascomycetes, although a great part of the fungal sequences remained unclassified. The number of archaeal 16S rRNA genes in the mine water was between 0.3 and 1.2 × 107copies mL−1in the samples from 500 m and 600 m, but only 3.9 × 103at 240 m and archaea were in general not enriched in cultures. The number of fungal 5.8S rRNA genes was high only in the mine water from 500 m and 600 m, where 0.2–3.4 × 104spore equivalents mL−1were detected. A high number ofLeptospirillum16S rRNA genes, 0.6–1.6 × 1010copies mL−1, were detected at 500 m and 600 m depth and in cultures containing ferrous iron, showing the importance of iron oxidizers in this environment. The abundance of bacteria in general was between 103and 10616S rRNA gene copies mL−1. Our results showed a high microbial diversity in the acid- and iron-impacted waters of the Pyhäsalmi mine, whereLeptospirillumbacteria were especially prominent. These iron oxidizers are also the main nitrogen-fixing microorganisms in this ecosystem.

scholarly journals Advantage of Using Inosine at the 3′ Termini of 16S rRNA Gene Universal Primers for the Study of Microbial Diversity

2006 ◽  
Vol 72 (11) ◽  
pp. 6902-6906 ◽  
Author(s):  
Eitan Ben-Dov ◽  
Orr H. Shapiro ◽  
Nachshon Siboni ◽  
Ariel Kushmaro
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Environmental Samples ◽  
Annealing Temperature ◽  
Universal Primers ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Primer Sets

ABSTRACT To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3′ termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging almost exclusively to Proteobacteria (95.8%). Sequences belonging to Firmicutes (42.6%) and Thermotogae (9.3%) were more abundant in a library obtained by using 8F-I/907R-I at a PCR annealing temperature of 54°C, while Proteobacteria sequences were more frequent (62.7%) in a library obtained at 50°C, somewhat resembling the result obtained using the original primer set. The increased diversity revealed by using primers 8F-I/907R-I confirms the usefulness of primers with inosine at the 3′ termini in studying the microbial diversity of environmental samples.

scholarly journals Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

2020 ◽  
Vol 21 (6) ◽  
pp. 1001-1010 ◽  
Author(s):  
Kathrin Busch ◽  
Lindsay Beazley ◽  
Ellen Kenchington ◽  
Frederick Whoriskey ◽  
Beate M. Slaby ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Anthropogenic Impacts ◽  
Anthropogenic Activities ◽  
Amplicon Sequencing ◽  
Habitat Destruction ◽  
Artificial Substrates ◽  
Rrna Gene ◽  
Anthropogenic Pressures ◽  
Glass Sponge

Abstract Establishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from protected sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in the four sponges from this site and the environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may ‘prime’ sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms.

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