Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow

Ghashghavi, Mohammad; Hester, Eric R.; Oliver, Viktoria; Lüke, Claudia; Jetten, Mike S. M.; Lücker, Sebastian

doi:10.1101/535229

Cited by 3 publications

(2 citation statements)

References 67 publications

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“…For example, the family Methylomonaceae was more abundant on parts of the shell with algae (mean=15.3 % of reads, sd =9.5) than on any other body area [mean per cent of reads (SD): buccal=0.7 % (0.5), head=3.3 % (2.3), shell without algae=7.9 % (11.8)]. Methylomonaceae are methanotrophic bacteria that occur in a variety of freshwater and marine environments, as well as in symbiotic relationships with deep-sea invertebrates living around thermal vents, and it is interesting to learn that they also colonize turtles’ shells (particularly areas with algae) [86–89]. Parts of the shell with algae also had the highest levels of bacteria in the family Saprospiraceae [mean per cent of reads ( sd ): buccal=0.3 % (0.4), head=3.6 % (2.3), shell without algae=6.4 % (2.7), shell with algae=14.1 % (2.5)], a group that is noted for its important role in breaking down complex organic molecules [90].…”

Section: Discussionmentioning

confidence: 99%

Microbiome diversity and composition varies across body areas in a freshwater turtle

et al. 2020

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There is increasing recognition that microbiomes are important for host health and ecology, and understanding host microbiomes is important for planning appropriate conservation strategies. However, microbiome data are lacking for many taxa, including turtles. To further our understanding of the interactions between aquatic microbiomes and their hosts, we used next generation sequencing technology to examine the microbiomes of the Krefft’s river turtle (Emydura macquarii krefftii). We examined the microbiomes of the buccal (oral) cavity, skin on the head, parts of the shell with macroalgae and parts of the shell without macroalgae. Bacteria in the phyla Proteobacteria and Bacteroidetes were the most common in most samples (particularly buccal samples), but Cyanobacteria , Deinococcus-thermus and Chloroflexi were also common (particularly in external microbiomes). We found significant differences in community composition among each body area, as well as significant differences among individuals. The buccal cavity had lower bacterial richness and evenness than any of the external microbiomes, and it had many amplicon sequence variants (ASVs) with a low relative abundance compared to other body areas. Nevertheless, the buccal cavity also had the most unique ASVs. Parts of the shell with and without algae also had different microbiomes, with particularly obvious differences in the relative abundances of the families Methylomonaceae, Saprospiraceae and Nostocaceae . This study provides novel, baseline information about the external microbiomes of turtles and is a first step in understanding their ecological roles.

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Section: Discussionmentioning

confidence: 99%

Microbiome diversity and composition varies across body areas in a freshwater turtle

et al. 2020

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“…The most represented identi ed family was the methylotrophic Methylomirabilaceae (∼10% of the reads in both samples) (Figure S1). This family was reported to be abundant in paddy elds, an anaerobic habitat typically rich in methane (Ghashghavi et al, 2019). The Sambaqui site explored in this study was built over a mangrove which is also considered a habitat with high methane production, this may explain the abundance of the methylotrophic Methylomirabilaceae in our samples.…”

Section: Prokaryotic Biodiversity Using 16s Rdna Amplicon Sequencingmentioning

confidence: 79%

The Microbiome of a Shell Mound: Ancient Anthropogenic Waste as a Source of Streptomyces Degrading Recalcitrant Polysaccharides

Huergo

Conzentino

Gonçalves

et al. 2021

Preprint

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Metagenome amplicon DNA sequencing and traditional cell culture techniques are helping to uncover the diversity and the biotechnological potential of prokaryotes in different habitats around the world. It has also had a profound impact on microbial taxonomy in the last decades. Here we used metagenome 16S rDNA amplicon sequencing to reveal the microbiome composition of different layers of an anthropogenic soil collected at a shell mound Sambaqui archeological site. The Samabaqui soil microbiome is mainly composed by phyla Acidobacteria, Rokubacteria, Proteobacteria and Thaumarchaeota. Using culture-dependent analysis we isolated few Streptomyces strains from the Sambaqui soil. One of the isolates, named Streptomyces sp. S3, was able to grow in minimal medium containing recalcitrant polysaccharides including chitin, xylan, carboxymethylcellulose or microcrystalline cellulose as sole carbon sources. The activities of enzymes degrading these compounds were confirmed in cell free supernatants. The genome sequence revealed not only an arsenal of genes related to polysaccharides degradation but also biosynthetic gene clusters which may be involved in the production of biotechnologically interesting secondary metabolites.

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The microbiome of a shell mound: ancient anthropogenic waste as a source of Streptomyces degrading recalcitrant polysaccharides

Huergo¹,

Conzentino²,

Gonçalves³

et al. 2021

World J Microbiol Biotechnol

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Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow

Abstract: 3 2 2

Cited by 3 publications

References 67 publications

Microbiome diversity and composition varies across body areas in a freshwater turtle

Microbiome diversity and composition varies across body areas in a freshwater turtle

The Microbiome of a Shell Mound: Ancient Anthropogenic Waste as a Source of Streptomyces Degrading Recalcitrant Polysaccharides

The microbiome of a shell mound: ancient anthropogenic waste as a source of Streptomyces degrading recalcitrant polysaccharides

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