Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench

Liu, Jiwen; Zheng, Yanfen; Lin, Heyu; Wang, Xuchen; Li, Meng; Liu, Yang; Meng, Yu; Zhao, Meixun; Pedentchouk, Nikolai; Lea‐Smith, David J.; Todd, Jonathan D.; Magill, Clayton R.; Zhang, Weijia; Zhou, Shun; Song, Delei; Zhong, Haohui; Xin, Yu; Yu, Min; Tian, Jie; Zhang, Xiaohua

doi:10.1186/s40168-019-0652-3

Cited by 139 publications

(178 citation statements)

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“…Additionally, the near bottom water of the Mariana Trench had more abundant culturable bacteria than the upper waters, according to our CFU count results, consistent with previous culture study results using the dilution counting method (Nunoura et al 2015). Indeed, at the near bottom water of the Trench, the abundance of total bacteria identified by the 16S rRNA gene qPCR method was also found to increase (Liu et al 2019c;Nunoura et al 2015), and the near bottom water was supposed to be dominated by heterotrophic bacteria (Nunoura et al 2015).…”

Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thesupporting

confidence: 91%

“…In this study, 825 bacterial strains (belonging to 108 genera and including 50 potential novel strains) were isolated from different water depths of the Mariana Trench. This culturable bacterial community was mainly composed of the phyla Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, which was similar to previous culture-independent studies by 16S rRNA genes high-throughput sequencing and metagenomics in the Mariana Trench (Liu et al 2019c;Nunoura et al 2015;Peoples et al 2018;Tarn et al 2016). At class level, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria_c, Bacilli and Flavobacteriia, which accounted for the majority of the culturable bacteria, were also the dominant classes (Liu et al 2019c;Nunoura et al 2015;Peoples et al 2018;Tarn et al 2016).…”

Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thesupporting

confidence: 85%

“…This difference between hadal and abyssal waters was also noted in previous studies with culture-independent data (Nunoura et al 2015;Peoples et al 2018). The abundance of Gammaproteobacteria, and thus heterotrophic activity, at the bottom of the trench was considered to be caused by organic matter sinking downward and funneling into the trench topography (Danovaro et al 2003;Glud et al 2013;Ichino et al 2015;Peoples et al 2018;Wenzhöfer et al 2016 (Liu et al 2019c;Peoples et al 2018;Tarn et al 2016). These results indicate that the culturable bacteria studied herein reliably reflect the total microbial communities of the Mariana Trench.…”

Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thesupporting

confidence: 66%

“…These genera have been previously found in deep-sea environments (Fan et al 2014;Lai et al 2009Lai et al , 2011Xu et al 2009) and some have been shown to have the ability to degrade (e.g., Lysinibacillus can degrade xylan, fomesafen and ethanethiol) (Lee et al 2010;Liang et al 2009;Wan et al 2010), indicating that they may have evolved specific strategies to survive in deep-sea environments such as the Mariana Trench. Some of the abundant groups in other culture-independent study, e.g., Epsilonproteobacteria and Cytophagia (Liu et al 2019c;Tarn et al 2016), were rare in the cultivation study reported here, indicating that the culture conditions still have many limitations. Different culture media and culture conditions will be necessary to obtain a more diverse bacterial community.…”

Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thementioning

confidence: 61%

“…Due to the rapid progress of deep-sea sampling techniques in recent years, the microbial community structures at different water depths of the Mariana Trench have been extensively studied by either 16S rRNA gene high-throughput sequencing (Nunoura et al 2015;Peoples et al 2018;Tarn et al 2016;Tian et al 2018) or metagenomic sequencing (Liu et al 2019c;Wang et al 2019). There have also Edited by Chengchao Chen.…”

Section: Introductionmentioning

confidence: 99%

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Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules

Zhao

Liu

Zhou

et al. 2020

Mar Life Sci Technol

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The Mariana Trench is the deepest location on earth and harbors unique microbial communities as evidenced by 16S rRNA gene amplicon and metagenomic sequencing. Obtaining culturable microorganisms from the Mariana Trench will contribute to a further understanding of hadal biogeochemical processes and act as a unique microbial reservoir with potential applications. Here, 825 bacterial strains, identified by 16S rRNA gene sequencing, were isolated from 12 water depths (0-10,400 m) of the Mariana Trench with 2216E and R2A media at 4 °C or 28 °C on four cruises during 2015-2017. These bacteria belong to four phyla, nine classes, 27 orders, 45 families and 108 genera. Alphaproteobacteria, Gammaproteobacteria, Actinobacteria_c, Bacilli and Flavobacteriia were the most abundant classes, accounting for 37.9%, 33.0%, 11.8%, 8.6% and 8.0% of the total bacterial isolates, respectively. 2216E and R2A media were found to have a better selectivity to Bacilli and Flavobacteriia, respectively. Fifty strains were potential novel bacterial species with a 16S rRNA gene similarity < 98.65%, and a higher percentage of novel strains were obtained from R2A than 2216E medium. Additionally, 301 (150 species) out of 354 strains (178 species) selected from each depth could degrade at least one of the ten kinds of macromolecules tested. These results indicate that there is a high diversity of culturable bacteria in the Mariana Trench and they can produce a variety of extracellular enzymes. Our study provides a valuable resource of microorganisms for investigating their biogeochemical roles in the Mariana Trench and for industrial applications.

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Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thesupporting

confidence: 91%

Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thesupporting

confidence: 85%

Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thesupporting

confidence: 66%

Section: Highly Diverse Heterotrophic Bacteria Were Obtained From Thementioning

confidence: 61%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules

Zhao

Liu

Zhou

et al. 2020

Mar Life Sci Technol

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Methane production in oxic seawater of the western North Pacific and its marginal seas

Wang

Zhang

et al. 2020

Limnology & Oceanography

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The oceans are natural sources of atmospheric methane (CH 4), but the origin of excess CH 4 at the surface remains enigmatic. Incubation experiments were conducted in the western North Pacific (WNP) and its marginal seas (i.e., Yellow Sea and South China Sea [SCS]) to identify the degradation of methylphosphonate (MPn) to CH 4 in the oceans and the microbes associated with MPn-driven CH 4 production. In the coastal seawater of the Yellow Sea, CH 4 was observed to accumulate after MPn enrichment with a high MPn to CH 4 conversion efficiency (approximately 60%). Dissolved inorganic phosphorus (Pi) did not effectively restrict the microbial utilization of MPn in the eutrophic coastal waters. The results of 16S rRNA gene sequencing showed that Vibrio spp. were the dominant bacteria in the MPn-amended treatments. Moreover, several Vibrio isolates isolated from the coastal waters were found to produce CH 4 while growing in culture using MPn as the sole P source, thereby indicating that Vibrio spp. might be the major contributors to MPn-dependent CH 4 production. In oligotrophic areas, such as the SCS and WNP, CH 4 production from MPn metabolism was also observed in the surface seawater. In contrast to coastal waters, this pathway in oligotrophic areas is regulated by dissolved Pi availability. This work confirms that aerobic CH 4 formation from MPn degradation can occur both in eutrophic coastal waters and oligotrophic oceans driven by MPn-utilizing microorganisms (especially heterotrophic bacteria), which may have a significant impact on our understanding of the CH 4 and P cycles in global oceans. Methane (CH 4) is a greenhouse gas that plays an important role in global warming. Oceans are a natural source of atmospheric CH 4 and contribute 1-4% of the annual global emissions (IPCC 2013). Studies have shown that the oxygenated surface waters throughout the majority of the global oceans are supersaturated with CH 4 with respect to the atmosphere, thereby implying a local CH 4 source. However, the origin of oceanic surface CH 4 is not sufficiently understood (Reeburgh 2007). Traditional CH 4 production is thought to be a strictly anaerobic process mediated by methanogenic archaea, which are outperformed by sulfate-reducing bacteria when competing for potential substrates (such as H 2 and acetate) (Sorokin et al. 2017). Methanogenesis appears to be inhibited by the presence of well-mixed oxygen and sulfate in the ocean surface. However, recent studies have shown that methylated compounds, such as

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High variability in organic carbon sources and microbial activities in the hadopelagic waters

Zhao

Dang

et al. 2023

Limnology & Oceanography

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Hadal sediments are recognized as organic carbon depocenters with intensified microbial activity compared to adjacent abyssal sites due to focusing of relatively labile organic materials. However, the sources and turnover of hadopelagic organic carbon and its linkages to microbial activities have not been studied. We present the first synergic research on particulate organic carbon, dark carbon fixation, and size‐fractionated microbial community respiration proxy over the Atacama Trench. The results demonstrate that all parameters attenuate rapidly from surface to mesopelagic water (~ 1000 m). Progressing deeper, values remain relatively stable throughout bathypelagic (~ 4000 m) and abyssopelagic (~ 6000 m) waters. However, in the hadopelagic zone (> 6000 m), highly variable values indicate dynamic organic carbon sources and microbial activities in the deepest trench. On average, 71% of the microbial community respiration proxy is attributable to particle‐associated communities, indicating importance of particles for microbial metabolism. No apparent relationship was observed between the microbial community respiration proxy and microbial 16S rRNA gene abundance below the epipelagic depth, indicating variable supply and quality of organic carbon likely constrained heterotrophic activities rather than microbial abundances in the deep ocean. The depth‐integrated dark carbon fixation (> 1000 m) accounts for 11.5% ± 7.6% of the surface net primary production, of which 2.9% ± 0.4% is from hadopelagic depth. Dark carbon fixation is thus an important in situ organic carbon source for hadal life. This study suggests that high variability in organic carbon sources and microbial activities in the hadopelagic trench cannot be simply extrapolated from findings in the shallower dark ocean (e.g., 1000–6000 m).

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Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench

Cited by 139 publications

References 50 publications

Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules

Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules

Methane production in oxic seawater of the western North Pacific and its marginal seas

High variability in organic carbon sources and microbial activities in the hadopelagic waters

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