Bacterial Diversity and Phylogenetic Analysis of Type II Polyketide Synthase Gene from Manao-Pee Cave, Thailand

Wiseschart, Apirak; Mhuanthong, Wuttichai; Thongkam, Pattamaporn; Tangphatsornruang, Sithichoke; Chantasingh, Duriya; Pootanakit, Kusol

doi:10.1080/01490451.2017.1411993

Cited by 10 publications

(19 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…When compared to the soil outside the cave, the cave soil is more brownish and sandy. In terms of geochemical composition, our previous study has shown that copper (Cu), iron (Fe), manganese (Mn), and zinc (Zn) were found at higher concentrations in soil samples from the cave [27]. Conversely, organic matter, total carbon, total nitrogen, and total hydrogen were found to be at lower concentrations when compared to soil samples outside the cave.…”

Section: Methodsmentioning

confidence: 99%

Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

et al. 2019

Self Cite

View full text Add to dashboard Cite

Background Due to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive. However, it has been well documented that microorganisms play important roles in cave development. Survival of microbes in this unique habitat likely involves a broad range of adaptive capabilities. Recently, cave microbiomes all over the world are of great scientific interest. However, the majority of investigations focused mostly on small subunit ribosomal RNA (16S rRNA) gene, leaving the ecological role of the microbial community largely unknown. Here, we are particularly interested in exploring the taxonomic composition and metabolic potential of microorganisms in soil from Manao-Pee cave, a subterranean limestone cave in the western part of Thailand, by using high-throughput shotgun metagenomic sequencing. Results From taxonomic composition analysis using ribosomal RNA genes (rRNA), the results confirmed that Actinobacteria (51.2%) and Gammaproteobacteria (24.4%) were the dominant bacterial groups in the cave soil community. Metabolic potential analysis, based on six functional modules of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, revealed that functional genes involved in microbial metabolisms are highly represented in this community (40.6%). To better understand how microbes thrive under unfavorable cave condition, we focused on microbial energy metabolism. The results showed that microbial genes involved in oxidative phosphorylation were the most dominant (28.8%) in Manao-Pee cave, and were followed by methane metabolism (20.5%), carbon fixation (16.0%), nitrogen metabolism (14.7%), and sulfur metabolism (6.3%). In addition, microbial genes involved in xenobiotic biodegradation (26 pathways) and in production of secondary metabolites (27 pathways) were also identified. Conclusion In addition to providing information on microbial diversity, we also gained insights into microbial adaptations and survival strategies under cave conditions. Based on rRNA genes, the results revealed that bacteria belonging to the Actinobacteria and Gammaproteobacteria were the most abundant in this community. From metabolic potential analysis, energy and nutrient sources that sustain diverse microbial population in this community might be atmospheric gases (methane, carbon dioxide, nitrogen), inorganic sulfur, and xenobiotic compounds. In addition, the presence of biosynthetic pathways of secondary metabolites suggested that they might play important ecological roles in the cave microbiome. Electronic supplementary material The online version of this article (10.1186/s12866-019-1521-8) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

“…Ikner et al (2007) suggested that the abundance of proteobacteria in caves could be as a result of increased organic input by cave visitors. Wiseschart et al (2018)…”

Section: Bacteria In Cavesmentioning

confidence: 99%

“…Echinamoeba silvestris is identified in the vicinity of speleothems in the epilithic algal community. These amoebae are known to occur at extreme environments, though they are regarded as non pathogenic (Walochnik and Mulec, 2015). They are all chemoheterotrophs.…”

Section: Protozoa In Cavesmentioning

confidence: 99%

“…Caves are oligotrophic, dark ecosystems providing extreme conditions (relatively constant low temperature and high relative humidity), for psychrophilic and psychrotolerant microorganisms that are able to grow in the environment (Wiseschart et al, 2018). Tomczyk-Żak and Zielenkiewicz (2016) reported that the limestone Kartchner cave has a humidity of 99.4%, temperature of 19.8 °C and a CO2 concentration from 1.000 to 5.000 ppm.…”

Section: Introductionmentioning

confidence: 99%

“…Leptospirillum sp., Thermodesulfovibrio sp., Candidata sp., Magnetobacterium sp., and Magnetoovum sp. Most of the isolated Actinobacteria is assigned to the genus Streptomyces in certain caves such as Grotta dei Cervi (Italy), Altamira and Tito Bustillo (Spain), and 19 karstic caves in Turkey(Kunisawa, 2010;Yucel and Yamac, 2010;Wiseschart et al, 2018). Acinetobacter sp., Stenotrophomonas sp., Sphingobacterium sp., Acinetobacter and Comamonas sp(Wiseschart et al, 2018).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Microbial communities and activities in caves

Raji¹,

Oyewole²,

Ibrahim³

et al. 2019

Braz. J. Biol. Sci.

View full text Add to dashboard Cite

Caves are natural aperture and oligotrophic extreme environment for psychrophilic and psychrotolerant microorganisms. Microorganisms found in caves can be indigenous to the caves or introduced by humans, animals, water flow and wind action. Group of microorganisms found in caves are bacteria, fungi, protozoa, algae and viruses. However, bacteria and fungi are the dominant microorganisms. Cave microorganisms are metabolically diverse and are able to acquire energy independently through photoautotrophic, chemoautotrophic or heterotrophic activities. Different microbial groups also interact in the formation of cave and as part of the biogeochemical cycling of elements. Cave microbiology has allowed the detection of microorganisms with the potentials to produce different biomolecules for industrial, pharmaceutical, environmental and biotechnological purposes.

show abstract

Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave

2020

View full text Add to dashboard Cite

Bacterial Diversity and Phylogenetic Analysis of Type II Polyketide Synthase Gene from Manao-Pee Cave, Thailand

Cited by 10 publications

References 62 publications

Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

Microbial communities and activities in caves

Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave

Contact Info

Product

Resources

About