Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia

Lau, Nyok-Sean; Zarkasi, Kamarul Zaman; Sah, Amir Shah Ruddin Md; Shu‐Chien, Alexander Chong

doi:10.1007/s00248-018-1283-0

Cited by 20 publications

(15 citation statements)

References 64 publications

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“…The longest contig was 408.1 kbp and the N50 was 748 bp. The performance of our assembly was slightly better than when the same assembler was used for a complex soil metagenome (Howe et al ; Li et al ), but comparable to other studies of sediments with the same assembler (e.g., Carr et al ; Lau et al ). We sorted the contigs into 1488 bins with < 10% contamination, of which 146 were at least “medium‐quality draft” assemblies with > 50% completion (after Bowers et al ).…”

Section: Resultssupporting

confidence: 73%

Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments

Ruuskanen

Colby

Pierre

et al. 2019

Limnology & Oceanography

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The Arctic is currently warming at an unprecedented rate, which may affect environmental constraints on the freshwater microbial communities found there. Yet, our knowledge of the community structure and functional potential of High Arctic freshwater microbes remains poor, even though they play key roles in nutrient cycling and other ecosystem services. Here, using high-throughput metagenomic sequencing and genome assembly, we show that sediment microbial communities in the High Arctic's largest lake by volume, Lake Hazen, are phylogenetically diverse, ranging from Proteobacteria, Verrucomicrobia, Planctomycetes, to members of the newly discovered Candidate Phyla Radiation groups. These genomes displayed a high prevalence of pathways involved in lipid chemistry, and a low prevalence of nutrient uptake pathways, which might represent adaptations to the specific, cold ($ 3.5 C) and extremely oligotrophic conditions in Lake Hazen. Despite these potential adaptations, it is unclear how ongoing environmental changes will affect microbial communities, the makeup of their genomic idiosyncrasies, as well as the possible implications at higher trophic levels.

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Section: Resultssupporting

confidence: 73%

Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments

Ruuskanen

Colby

Pierre

et al. 2019

Limnology & Oceanography

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“… 20 In addition, some studies have reported the dominance of Verrucomicrobia followed by Proteobacteria and Bacteroidetes in aquaculture systems. 21 , 22 The GLM suggested that the proportion of Proteobacteria and Bacteroidetes did not differ among fish types, whereas that of Verrucomicrobia in the G. punctata tank was larger ( Table S1 ), suggesting that Verrucomicrobia might be a more host-specific phylum in the rearing water. At the genus level, Sediminicola , Glaciecola , unassigned Saprospiraceae , and Rubritalea exceeded 50% of relative abundance, whereas such dominance varied with sample ( Figure 1 A).…”

Section: Resultsmentioning

confidence: 99%

Microbiome and Metabolome Analyses in Different Closed-Circulation Aquarium Systems and Their Network Visualization

et al. 2022

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Understanding the causes of microbiome formation and its relationship to environmental conditions is important to properly maintain recirculating aquaculture systems (RASs). Although RAS has been applied to numerous fish types and environmental conditions (e.g., loading intensity), the effects of these environmental conditions (i.e., fish type and loading intensity) on microbiome composition are limitedly known. Therefore, we established three experimental aquarium tanks to explore the effects of fish type, loading intensity, filter pore size, and rearing day on microbiome compositions: (1) a tank for Acanthogobius flavimanus , (2) for Girella punctata , and (3) for G. punctata with higher loading intensity. Multivariate analysis showed that the microbial community composition differed among the tanks, indicating that the fish type and loading intensity significantly affected microbiome formation in rearing water. Some microbes, such as Sediminicola and Glaciecola , were detected at a higher loading intensity, indicating that these microbes might be an indicator of eutrophic conditions in the aquacultural systems. In addition, a partial correlation network revealed a connection between microbes and metabolites in the aquarium tanks. Such a microbe–metabolite network might be a clue to control the microbiome by adjusting the molecule abundance in the aquacultural environment.

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“…Lau et al . (2019) reported that the photic water layer in Temengor Lake, Malaysia was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages; in contrast, the aphotic water featured Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla (Chloroflexi and Firmicutes) that are typically ubiquitous in anoxic habitats. Proteobacteria also dominated intestinal bacteria in white shrimp and sediment bacteria in freshwater and seawater culture ponds (Fan et al .…”

Section: Resultsmentioning

confidence: 99%

Planktonic bacteria in white shrimp ( Litopenaeus vannamei ) and channel catfish ( Letalurus punetaus ) aquaculture ponds in a salt‐alkaline region

Zhao

Guan

et al. 2021

Letters Applied Microbiology

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Aquaculture in salt‐alkaline regions is encouraged in China, and culture of many aquatic species has been introduced into these areas. In this study, we cultured two species, white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) separately in aquaculture ponds in a salt‐alkaline region in northwest China and assessed the impacts of the aquaculture operations on the planktonic bacterial community in the culture ponds. Culture of both species decreased the planktonic bacterial diversity and altered the bacterial community structure in the aquaculture ponds compared with the source water. Among the 10 dominant bacterial phyla, 8 were significantly correlated with environmental parameters; the exception was Actinobacteriota, the most dominant phylum, and Firmicutes. Proteobacteria and Bacteroidota abundances showed significant positive correlations with alkalinity, whereas Patescibacteria, Cyanobacteria, Planctomycetota, and Verrucomicrobiota abundance were positively correlated with salinity. Linear regression analysis showed that alkalinity was positively correlated with bacterial beta diversity and salinity was negatively correlated with that. In addition, white shrimp aquaculture significantly lowered the alkalinity, which suggests that culture of this species in inland salt‐alkaline regions is a potential dealkalization solution.

show abstract

Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia

Cited by 20 publications

References 64 publications

Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments

Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments

Microbiome and Metabolome Analyses in Different Closed-Circulation Aquarium Systems and Their Network Visualization

Planktonic bacteria in white shrimp ( Litopenaeus vannamei ) and channel catfish ( Letalurus punetaus ) aquaculture ponds in a salt‐alkaline region

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