Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand

Somboonna, Naraporn; Assawamakin, Anunchai; Wilantho, Alisa; Tangphatsornruang, Sithichoke; Tongsima, Sissades

doi:10.1186/1471-2164-13-s7-s29

Cited by 43 publications

(51 citation statements)

References 66 publications

(98 reference statements)

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“…Among the 18S rDNA sequences, it was found that fungi, mainly the Basidiomycota, accounted for around 75% of the organisms detected in Tha Wang Bay. Constrastingly, fungi were ten times less abundant in Tham Phang Bay [43], in which over 80% of the 18S rDNA sequences were assigned to Metazoa (specifically to Brachiopoda and Mollusca). Another comparative metagenomics study, conducted in the Sea of Marmara, found out that Fungi and Metazoa represented 30% of the total sequences obtained from sediment samples, but these organisms were poorly represented in the bathypelagic planktonic samples [51].…”

Section: Watermentioning

confidence: 97%

“…Approximately 71% and 0.8% of the Earth's area is covered by saltwater and freshwater, respectively [43,44]. These ecosystems are regarded as the largest bioproductive resources, and oceanic microorganisms are responsible for up to 98% of primary production [45].…”

Section: Watermentioning

confidence: 99%

“…The fungal abundance in aquatic ecosystems can vary greatly, and the environmental community profile can be influenced by sampling methods [50] and environmental conditions, including anthropogenic activity [43]. A study conducted in Sichang Island (Thailand) using pyrotag sequencing compared the metagenomes of two coastal areas with similar oceanographic positions, which differ in bay geography and the extent of municipal disturbances [43]. Among the 18S rDNA sequences, it was found that fungi, mainly the Basidiomycota, accounted for around 75% of the organisms detected in Tha Wang Bay.…”

Section: Watermentioning

confidence: 99%

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Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Cuadros-Orellana¹

2013

Fungal Genom Biol

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Fungi are ubiquitous inhabitants of soil and aquatic environments, and they establish and maintain either parasitic or symbiotic relationships with animals and plants. They are major players in nutrient cycling, especially in organic matter decomposition, and they are major sources of biologically active substances. However, their full metabolic potential is yet to be unveiled, and fungal enzymes could be of great use in myriad of applications from industrial processes to natural products. The global number of species in the fungal kingdom has been estimated in the range of one to a few million, but it is likely larger, as suggested by recent metagenomic studies that revealed the existence of fungal diversity hotspots. In this review, we describe the main advances in the study of fungal diversity, present statistics of the main metagenomic databases with regard to the representativeness of fungal phyla, and discuss the future directions in this field.

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Section: Watermentioning

confidence: 97%

Section: Watermentioning

confidence: 99%

Section: Watermentioning

confidence: 99%

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Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Cuadros-Orellana¹

2013

Fungal Genom Biol

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“…This diversity concerns microbial eukaryotes as well (nematodes, protists, fungi), found in marine sediments, which can play pivotal roles in maintaining ecosystem function [125]. Archaea have also been described in sediments [126,127]. Investigations in ponds [128] and oceans [129] have also highlighted an unknown and rapid turnover of viruses and microorganisms.…”

Section: How To Use Metagenomics?mentioning

confidence: 99%

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?

Bastaraud

Cecchi

Handschumacher

et al. 2020

IJERPH

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A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.

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“…Also, these pollutants have the potential to exert selective pressure on microbial communities found therein. For instance, some studies suggest that the microbial abundance, as well as diversity in the aquatic environment, is influenced by various environmental parameters such as pH, temperature, DO, and salinity [4,5]. However, whichever geochemical parameter could be the primary determinant of microbial community composition, the presence or absence of particular nutrients or contaminants in the environment can potentially alter the microbial ecological niche, resulting in a direct impact on microbial community structure [6].…”

Section: Introductionmentioning

confidence: 99%

Industrial Effluents Harbor a Unique Diversity of Fungal Community Structures as Revealed by High-throughput Sequencing Analysis

Selvarajan¹,

Sibanda²,

Sekar³

et al. 2019

Pol. J. Environ. Stud.

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The actual extent of fungal diversity in different environmental media is still a subject of ongoing research. Little is currently known about the diversity of fungal populations in industrial streams. This study characterized the fungal diversity of different industrial effluents using a high-throughput sequencing approach. A total of 234617 quality filtered reads were obtained from the collected wastewater samples. Phylogenetic taxonomy revealed that resident fungal communities were classified as 6 phyla, 31 classes, 79 orders, 144 families, and 192 genera. Ascomycota and Basidiomycota were the most dominant phyla whose relative abundance ranged from 23.29% to 38.31%, and 17.34% to 33.51%, respectively. Recovered operational taxonomic units (OTUs) ranged from 292 (Dixon) to 427 (Capegate). The existence of some fungal genera identified in the industrial wastewaters correlated to physicochemical variables and had the potential to play important roles in organic decomposition, pollutant degradation, and xenobiotic transformation. Meanwhile, the occurrence of unclassified fungal sequences (22.5% to 33.09%) suggests that these effluents are a potential reservoir of as-yet uncharacterized fungal species.

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Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand

Cited by 43 publications

References 66 publications

Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?

Industrial Effluents Harbor a Unique Diversity of Fungal Community Structures as Revealed by High-throughput Sequencing Analysis

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