Diversity and community composition of particle‐associated and free‐living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait

Milici, Mathias; Vital, Marius; Tomasch, Jürgen; Badewien, Thomas H.; Giebel, Helge-Ansgar; Plumeier, Iris; Wang, Hui; Pieper, Dietmar H.; Wagner‐Döbler, Irene; Simon, Meinhard

doi:10.1002/lno.10487

Cited by 70 publications

(86 citation statements)

References 85 publications

(136 reference statements)

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“…The PA fraction is relatively enriched in members of γ-Proteobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes and Planctomycetes (Azam and Malfatti, 2007;Milici et al, 2016;Salazar et al, 2016;Suter et al, 2018), while the FL assemblages are often populated by members of α-Proteobacteria (SAR11 clade or Ca. Pelagibacter) and Deferribacteres (DeLong et al, 1993;Crespo et al, 2013;Milici et al, 2017). However, significantly overlapped compositions of PA and FL microbial communities were also reported in a few studies (Hollibaugh et al, 2000;Ghiglione et al, 2007;Ortega-Retuerta et al, 2013;Rieck et al, 2015;Liu et al, 2018a).…”

Section: Introductionmentioning

confidence: 76%

“…4). Recent studies have shown that microbial populations in the meso-/ bathypelagic ocean are largely dissimilar to those of the epipelagic zone (Salazar et al, 2015;Milici et al, 2017;Liu et al, 2018a), indicative of a crucial environmental selection process exerted by depth.…”

Section: Environmental Factors Potentially Shaping Microbial Communitmentioning

confidence: 99%

“…CC BY 4.0 License. et al, 2015;Salazar et al, 2015;Milici et al, 2017;Mestre et al, 2018) or the deepest abyssal and hadal environments (Eloe et al, 2011;Tarn et al, 2016;Liu et al, 2018a). It is shown that PA and FL bacterial communities in the deep ocean have clear differences in abundance and composition, in addition to the detection of novel, unknown prokaryotic taxa.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea

Li¹,

Gu²,

Bai³

et al. 2020

Preprint

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Abstract. There is a growing recognition of the role of particle-attached (PA) and free-living (FL) microorganisms in marine carbon cycle. However, current understanding of PA and FL microbial communities is largely on those in the upper photic zone, and relatively fewer studies have focused on microbial communities of the deep ocean. Moreover, archaeal populations receive even less attention. In this study, we determined bacterial and archaeal community structures of both the PA and FL assemblages at different depths, from the surface to the bathypelagic zone along two water column profiles in the South China Sea. Our results suggest that environmental parameters including depth, seawater age, salinity, POC, DOC, DO and silicate play a role in structuring these microbial communities. Generally, the PA microbial communities have relatively low abundance and diversity compared with the FL microbial communities at most depths. Further microbial community analysis revealed that PA and FL fractions generally accommodate significantly divergent microbial compositions at each depth. The PA bacterial communities mainly comprise members of Actinobacteria and γ-Proteobacteria, together with some from Bacteroidetes, Planctomycetes and δ-Proteobacteria, while the FL bacterial lineages are mostly distributed within α-, γ-Proteobacteria, Actinobacteria and Bacteroidetes, along with certain members from β-, δ-Proteobacteria, Planctomycetes and Firmicutes. Moreover, there is an obvious shifting in the dominant PA and FL bacterial compositions along the depth profiles from the surface to the bathypelagic deep. By contrast, both PA and FL archaeal communities dominantly consist of Marine Group II (MGII) and Marine Group I (MGI), together with variable minor Marine Group III (MGIII), Methanosarcinales, Marine Benthic Group A (MBG-A) and Woesearchaeota. However, the pronounced distinction of archaeal community compositions between PA and FL fractions are observed at finer taxonomic level. A high proportion overlap of microbial compositions between PA and FL fractions implies that most microorganisms are potentially generalists with PA and FL dual lifestyle for versatile metabolic flexibility. In addition, microbial distribution along the depth profile indicates a potential vertical connectivity between the surface-specific microbial lineages and those in the deep ocean, likely through microbial attachment to sinking particles.

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Section: Introductionmentioning

confidence: 76%

Section: Environmental Factors Potentially Shaping Microbial Communitmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea

Li¹,

Gu²,

Bai³

et al. 2020

Preprint

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“…Below the euphotic and 1% irradiance layers (aphotic, 150 to 5,125 m), the relative and absolute abundances of well-known mesopelagic bacterial clades, SAR324, SAR406, SAR202, Sulfitobacter, and the SVA0996 marine group, increased ( Fig. 3b and c) (20)(21)(22). In addition to the bacterial clades with high read abundances, there was also a large rare bacterial community throughout the SPG (relative read abundance of Ͻ0.1%).…”

mentioning

confidence: 98%

On-Site Analysis of Bacterial Communities of the Ultraoligotrophic South Pacific Gyre

Reintjes

Tegetmeyer

Bürgisser

et al. 2019

Appl Environ Microbiol

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The South Pacific Gyre (SPG) covers 10% of the ocean's surface and is often regarded as a marine biological desert. To gain an on-site overview of the remote, ultraoligotrophic microbial community of the SPG, we developed a novel onboard analysis pipeline, which combines next-generation sequencing with fluorescence in situ hybridization and automated cell enumeration. We tested the pipeline during the SO-245 "UltraPac" cruise from Chile to New Zealand and found that the overall microbial community of the SPG was highly similar to those of other oceanic gyres. The SPG was dominated by 20 major bacterial clades, including SAR11, SAR116, the AEGEAN-169 marine group, SAR86, Prochlorococcus, SAR324, SAR406, and SAR202. Most of the bacterial clades showed a strong vertical (20 m to 5,000 m), but only a weak longitudinal (80°W to 160°W), distribution pattern. Surprisingly, in the central gyre, Prochlorococcus, the dominant photosynthetic organism, had only low cellular abundances in the upper waters (20 to 80 m) and was more frequent around the 1% irradiance zone (100 to 150 m). Instead, the surface waters of the central gyre were dominated by the SAR11, SAR86, and SAR116 clades known to harbor light-driven proton pumps. The alphaproteobacterial AEGEAN-169 marine group was particularly abundant in the surface waters of the central gyre, indicating a potentially interesting adaptation to ultraoligotrophic waters and high solar irradiance. In the future, the newly developed community analysis pipeline will allow for on-site insights into a microbial community within 35 h of sampling, which will permit more targeted sampling efforts and hypothesis-driven research.

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“…NS4 marine group bacteria within the phylum Bacteroidetes are commonly detected in marine microbial communities (Alonso et al 2007;Becker et al 2017;Milici et al 2017) and exhibit seasonality in some environments (Alonso-Saez et al 2015). Bacteria within the "Ca.…”

Section: Heterogeneity In Bacterial and Archaeal Diversity And Composmentioning

confidence: 99%

Characterizing the ecology of coral reef microorganisms across different scales within the Caribbean

Weber¹

2020

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Microorganisms sustain the high productivity of coral reefs and support one of the most diverse, valuable, and threatened ecosystems on Earth. Despite the importance of reef microorganisms, there is a lack of understanding about their ecology, especially on Caribbean reefs. Furthermore, the hastening degradation of reefs due to anthropogenic stressors has made it difficult to understand natural patterns in microbial communities in the context of larger-scale ecosystem changes. Using genomics and metabolomics approaches paired with biogeochemical and physicochemical measurements as well as quantification of cell abundances, this dissertation provides optimized methods for studying the coral microbiome, investigates potential interactions between corals and seawater microorganisms, measures changes in the composition and diversity of reef seawater microorganisms over different spatial and temporal scales, and provides baseline information about microbial ecology, biogeochemistry, and metabolite compositions of a protected and relatively-healthy Cuban coral reef-system to fill these critical knowledge gaps. I found that coral species and reef location influenced the composition of bacteria and archaea within the seawater surrounding coral colonies and this seawater was enriched with microbial colonization and interaction genes, providing evidence of a distinct microbial environment surrounding corals named the coral ecosphere. In a separate study, diel and daily variation superseded spatial variation in terms of influencing shifts in the microbial community. At a larger scale, seawater microbial communities collected from the protected reefsystem of Jardines de la Reina, Cuba had higher alpha diversity and community similarity, lower nutrient concentrations, and higher abundances of picocyanobacteria compared to less protected reef-systems within Los Canarreos, Cuba and the Florida Keys, U.S.A and seawater microbial communities collected from each reef-system were influenced by hydrogeography and environmental gradients. Lastly, the extracellular metabolite composition of reef seawater collected across Jardines de la Reina was highly similar, suggesting homogenous environmental and hydrogeographic conditions across these forereefs. Overall, this dissertation characterizes reef seawater microbial communities across different scales and provides novel, baseline information about a protected and understudied Cuban reef-system, offering critical information about the ecology of reef microorganisms within the Caribbean.Thesis Supervisor: Dr. Amy Apprill Title: Associate Scientist Woods Hole Oceanographic Institution Kelly et al. 2014;, potentially leading to further reef degradation.As a result of these anthropogenic-induced changes, there is a pressing need to address fundamental questions about reef microbial community ecology from relatively healthy reefs to provide baseline information about the composition, diversity, function, and variations of these communities. The goals of this dissertation were to provide crit...

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Diversity and community composition of particle‐associated and free‐living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait

Cited by 70 publications

References 85 publications

Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea

Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea

On-Site Analysis of Bacterial Communities of the Ultraoligotrophic South Pacific Gyre

Characterizing the ecology of coral reef microorganisms across different scales within the Caribbean

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