Comparative analysis of deep-sea bacterioplankton OMICS revealed the occurrence of habitat-specific genomic attributes

Abstract

Bathyal aphotic ocean represents the largest biotope on our planet, which sustains highly diverse but low-density microbial communities, with yet untapped genomic attributes, potentially useful for discovery of new biomolecules, industrial enzymes and pathways. In the last two decades, culture-independent approaches of high-throughput sequencing have provided new insights into structure and function of marine bacterioplankton, leading to unprecedented opportunities to accurately characterize microbial communities and their interactions with the environments. In the present review we focused on the analysis of relatively few deep-sea OMICS studies, completed thus far, to find the specific genomic patterns determining the lifeway and adaptation mechanisms of prokaryotes thriving in the dark deep ocean below the depth of 1000m. Phylogenomic and omic studies provided clear evidence that the bathyal microbial communities are distinct from the epipelagic counterparts and, along with generally larger genomes, possess their own habitat-specific genomic attributes. The high abundance in the deep ocean OMICS of the systems for environmental sensing, signal transduction and metabolic versatility as compared to the epipelagic counterparts is thought to enable the deep-sea bacterioplankton to rapidly adapt to changing environmental conditions associated with resource scarcity and high diversity of energy and carbon substrates in the bathyal biotopes. Together with a versatile heterotrophy, mixotrophy and anaplerosis are thought to enable the deep-sea bacterioplankton to cope with these environmental conditions.

Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea

“…The class γ- Proteobacteria constituted only a minor fraction in our molecular-based study, although members of this class are best known for their rapid growth and also represented as a major group in global surveys ( Pommier et al, 2007 ). OTUs assigned to α- Proteobacteria and Cyanobacteria phyla were cosmopolitans in our study, and this finding is consistent with previous reports ( Pommier et al, 2007 ; Smedile et al, 2014 ). Cyanobacteria dominated at W1 and W4 stations and most OTUs belonged to the genus Synechococcus .…”

“…As far as the littoral area of Bohai Sea is concerned, this is one of the first studies to our knowledge which reports the diversity of the bacterioplankton assemblage nearby harbor and the factors that shape their structure and composition. Proteobacteria, Cyanobacteria, Actinobacteria , and Bacteroidetes represented the major phylotypes at the 6 stations, and is in agreement with other reports which have found these bacterioplankton groups to be the major inhabitant of marine habitats ( Li J. et al, 2011 ; Li et al, 2013 ; Smedile et al, 2014 ; Xiong et al, 2015 ; Jeffries et al, 2016 ). Proteobacteria and Cyanobacteria exhibited higher dynamics in their composition among others.…”

Uptake‐release dynamics of the inorganic and organic carbon pool mediated by planktonic prokaryotes in the deep Mediterranean Sea

“…We speculate that these differences should be attributed to the persistently higher temperature that characterizes the meso‐and bathypelagic Mediterranean (> 12°C vs 0‐4°C found in other systems) or to structurally diverse assemblages involved in the process. It is known that the Mediterranean Sea can be considered as a peculiar oceanic region as highlighted by its metagenomic fingerprint (Sunagawa et al ., ), including the dark portion of the water column (Martín‐Cuadrado et al ., ; Smedile et al ., ; Luna, ). Both these aspects are known to affect the bulk microbial metabolism (Pomeroy and Wiebe, ; Kirchman, ), although no direct evidence of their strength have been provided for dark primary production.…”

Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly

“…For example, higher availability of aromatic compounds such as aromatic carboxylic humic acids in soil ( Van Trump et al, 2011 ) plays an important role in enriching genes involved in aerobic degradation of aromatic compounds (group D; Supplementary Figure S16B ). In marine environments, high concentrations of nitrate and nitrite in euphotic and mesopelagic zones below the nitracline ( Shi et al, 2010 ) and extreme oligotrophy in deep sea ( Smedile et al, 2014 ) are important for enriching genes involved in nitrogen metabolism, bacterial chemotaxis, and flagellar assembly (group B; Supplementary Table S11 ). Therefore, it is not surprising that many marine bacteria are motile, with the proportion of motile cells being as high as 20–60% ( Stocker, 2012 ).…”