Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning

Graham, Elaina D.; Tully, Benjamin J.

doi:10.1101/2020.06.22.165886

Cited by 12 publications

(11 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Chlamydiae, known as human obligate intracellular pathogens, were found only in one freshwater sample [ 51 ], while some phyla, i.e., Dadabacteria and Hydrogenedentes, only in seawater PE wastes. Our results confirm those obtained by recent studies on Dadabacteria, considered as cosmopolitan bacteria of the marine environment [ 52 ] and Hydrogenedentes, assumed as putative organic carbon degraders, potentially hydrolyzing carbon compounds such as phthalates, of which plastics are made of [ 53 ].…”

Section: Discussionsupporting

confidence: 91%

A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea

Sucato

Vecchioni

Savoca

et al. 2021

Biology

View full text Add to dashboard Cite

In this study, we evaluated the microbiome and the resistome profile of water and fragments of polyethylene (PE) waste collected at the same time from a stream and the seawater in a coastal area of Northwestern Sicily. Although a core microbiome was determined by sequencing of the V3–V4 region of the bacterial 16S rDNA gene, quantitative differences were found among the microbial communities on PE waste and the corresponding water samples. Our findings indicated that PE waste contains a more abundant and increased core microbiome diversity than the corresponding water samples. Moreover, PCR analysis of specific antibiotic resistance genes (ARGs) showed that PE waste harbors more ARGs than the water samples. Thus, PE waste could act as a carrier of antibiotic-resistant microbiota, representing an increased danger for the marine environment and living organisms, as well.

show abstract

Section: Discussionsupporting

confidence: 91%

A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea

Sucato

Vecchioni

Savoca

et al. 2021

Biology

View full text Add to dashboard Cite

show abstract

“…The copyright holder for this preprint (which this version posted April 10, 2021. ; https://doi.org/10.1101/2021.04.08.436999 doi: bioRxiv preprint contrasts of these taxa were stronger in the WSC (average Kruskal-Wallis significance p ≤ 0.003 vs. 0.02 in the EGC). Furthermore, Dadabacteriales co-occurred from February (WSC) or late March (EGC) and might contribute to the recycling of microbial and other organic matter 70 . Fundamental regional differences were the heterotrophic "recycling state" in the WSC compared to ice-related microbial signatures in the EGC.…”

Section: Wintermentioning

confidence: 99%

The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean

Wietz¹,

Bienhold²,

Metfies³

et al. 2021

Preprint

View full text Add to dashboard Cite

Change is a constant in the Arctic Ocean, with extreme seasonal differences in daylight, ice cover and temperature. The biodiversity and ecology of marine microbes across these extremes remain poorly understood. Here, using an array of autonomous samplers and sensors, we portray an annual cycle of microbial biodiversity, nutrient budgets and oceanography in the major biomes of the Fram Strait. In the ice-free West Spitsbergen Current, community turnover followed the solar cycle, with distinct separation of a productive summer state dominated by diatoms and carbohydrate-degrading bacteria, and a regenerative winter state dominated by heterotrophic Syndiniales, radiolarians, chemoautotrophic bacteria and archaea. Winter mixing of the water column replenishing nitrate, phosphate and silicate, and the onset of light were the major turning points. The summer succession of Phaeocystis, Grammonema and Thalassiosira coincided with ephemeral peaks of Formosa, Polaribacter and NS clades, indicating metabolic relationships between phytoplankton and bacteria. In the East Greenland Current, ice cover and greater sampling depth coincided with weaker seasonality, featuring weaker bloom/decay events and an ice-related winter microbiome. Low ice cover and advection of Atlantic Water coincided with diminished abundances of chemoautotrophic bacteria while Phaeocystis and Flavobacteriaceae increased, suggesting that Atlantification alters phytoplankton diversity and the biological carbon pump. Our findings promote the understanding of microbial seasonality in Arctic waters, illustrating the ecological importance of the polar night and providing an essential baseline of microbial dynamics in a region severely affected by climate change.

show abstract

“…Appealingly, the Dadabacteria have the potential to degrade microbial particulate organic matter, particularly peptidoglycan and phospholipids. The marine Dadabacteria were divided into two clades with distinctive ecological niches in worldwide metagenomic data: a shallow clade with the potential for photoheterotrophy through the utilization of proteorhodopsin, exist principally in surface waters up to 100m depth; and a deep clade that is more varied in the deep photic zone without the photoheterotrophic potential (Graham, Tully, 2020).…”

Section: Resultsmentioning

confidence: 99%

Bioinformatic approaches for analysis of coral-associated bacteria using R programming language

Nhung¹,

Ngoc²

2021

Vietnam J. Biotechnol.

View full text Add to dashboard Cite

Recent advances in metagenomics and bioinformatics allow the robust analysis of the composition and abundance of microbial communities, functional genes, and their metabolic pathways. So far, there has been a variety of computational/statistical tools or software for analyzing microbiome, the common problems that occurred in its implementation are, however, the lack of synchronization and compatibility of output/input data formats between such software. To overcome these challenges, in this study context, we aim to apply the DADA2 pipeline (written in R programming language) instead of using a set of different bioinformatics tools to create our own workflow for microbial community analysis in a continuous and synchronous manner. For the first effort, we tried to investigate the composition and abundance of coral-associated bacteria using their 16S rRNA gene amplicon sequences. The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case. The outcomes obtained in this study suggest that the DADA2 pipeline written in R programming language is one of the potential bioinformatics approaches in the context of microbiome analysis other than using various software. Besides, our modifications for the workflow execution help researchers to illustrate metagenomic data more easily and systematically, elucidate the composition, abundance, diversity, and relationship between microorganism communities as well as to develop other bioinformatic tools more effectively.

show abstract

Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning

Abstract: 9

Cited by 12 publications

References 49 publications

A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea

A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea

The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean

Bioinformatic approaches for analysis of coral-associated bacteria using R programming language

Contact Info

Product

Resources

About