Scientific and technological progress in the microbial exploration of the hadal zone

Fan, Shen; Wang, Meng; Ding, Wei; Li, Yong-Xin; Zhang, Yuzhong; Zhang, Weipeng

doi:10.1007/s42995-021-00110-1

Cited by 11 publications

(7 citation statements)

References 122 publications

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“…Presence of hydrocarbons at the trench bottom could be due both to xenobiotic (e.g., oil spill falls) and biotic (from heterotrophic and autotrophic organisms) sources revealed in sinking particles [ 18 ]. Thus, the occurrence of the hydrocarbonoclastic bacteria in the KKT samples is consistent with what found for other trench environments: the deepest zones support the growth of these heterotrophic microorganisms that locally contribute to hydrocarbon recycle at the bottom of the ocean [ 3 , 99 ].…”

Section: Resultssupporting

confidence: 80%

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

Gorrasi

Franzetti

Brandt

et al. 2023

Environmental Microbiome

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Background The Kuril–Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment. Results As for the bacterial communities, we found that Proteobacteria (56.1–74.5%), Bacteroidetes (6.5–19.1%), and Actinobacteria (0.9–16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9–91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril–Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench. Conclusions This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril–Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.

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Section: Resultssupporting

confidence: 80%

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

Gorrasi

Franzetti

Brandt

et al. 2023

Environmental Microbiome

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“…Despite the increasing number of the global ocean omics studies, there are still many types of ocean microbiota that are barely studied, such as the gut microbiota of animals, especially those living in the deep sea [ 92 , 93 , 94 ]. Here, we would like to highlight a recent study [ 95 ] in which more than 5000 genomes comprising the intestinal microflora of 180 wild animals living on land were analyzed, including different species, feeding behavior, geographical locations, and characteristics.…”

Section: Bottlenecks and Future Directionsmentioning

confidence: 99%

The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms

Shu

Zhang

et al. 2023

IJMS

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The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.

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“…While the above-mentioned studies have provided insights into the impact of ammonia on shrimp, very little attention has been paid to the effect of ammonia on the shrimp gut microbiota. The gut microbiota, as a kind of microbial biofilm, has been known to play important roles in dealing with environmental stimuli and in helping the host adapt to a variety of environments [ 15 , 16 , 17 ]. In one study, exposure to ammonia resulted in taxonomic abundance and composition variations in the gut microbiota of L. vannamei [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Acute Ammonia Causes Pathogenic Dysbiosis of Shrimp Gut Biofilms

Gao,

Shu,

Wang

et al. 2024

IJMS

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Acute ammonia exposure has detrimental effects on shrimp, but the underlying mechanisms remain to be fully explored. In the present study, we investigated the impact of acute ammonia exposure on the gut microbiota of the white shrimp Litopenaeus vannamei and its association with shrimp mortality. Exposure to a lethal concentration of ammonia for 48 h resulted in increased mortality in L. vannamei, with severe damage to the hepatopancreas. Ammonia exposure led to a significant decrease in gut microbial diversity, along with the loss of beneficial bacterial taxa and the proliferation of pathogenic Vibrio strains. A phenotypic analysis revealed a transition from the dominance of aerobic to facultative anaerobic strains due to ammonia exposure. A functional analysis revealed that ammonia exposure led to an enrichment of genes related to biofilm formation, host colonization, and virulence pathogenicity. A species-level analysis and experiments suggest the key role of a Vibrio harveyi strain in causing shrimp disease and specificity under distinct environments. These findings provide new information on the mechanism of shrimp disease under environmental changes.

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Scientific and technological progress in the microbial exploration of the hadal zone

Cited by 11 publications

References 122 publications

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms

Acute Ammonia Causes Pathogenic Dysbiosis of Shrimp Gut Biofilms

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