Microbial mysteries on deep sea !!!

“The microbial environment deep beneath the seafloor may provide a window into how organisms could survive in places beyond Earth” (Meyer, 2012)

Deep sea exploration presents different challenges more than answers, however the fascinating hidden microbial world of deepest side of the ocean is an interesting topic to research life on Earth. Different questions remain to be answered and are key to understand the microbial component on this hostile environment, how deep are found microbial forms on the sea?  What are the patterns in the distribution, diversity and dominance of functional and taxonomic groups of bacteria at the vast ocean seafloor? What is the role of microbial component on biogeochemical cycles on the seafloor? Are bacterial communities in symbiosis with different host animals?  And how is it possible to maintain functions in microbial cells at an energy flux that barely allows cell growth over tens to thousands of years?¹. All these enigmas could be resolved using exploration technology and molecular techniques for revel microbial deep sea mysteries.

The deep sea floor is widely regarded as the largest ecosystem on Earth ², covering around 65% of the planet’s surface ³. The world’s oceans are teeming with microscopic life forms where bacteria, archaea, protists, and unicellular fungi account for most of the oceanic biomass ⁴.  Besides the hostile environment of deep-sea, there are diverse landscapes of canyons, cold seeps, deep-water coral reefs, mud volcanoes, carbonate mounds, brine pools, gas hydrates, seamounts, ridges, fractures and trenches that are host to rich microbial communities¹ (Figure 1) with several adaptations for resist environmental conditions, using it’s metabolic mechanisms.  

Figure 1. Microbial ecosystems. A) Microbial mat at Haakon Mosby Mud Volcano. B) A methanotrophic microbial reef of the Black Sea. C) Microbial mat above oily sediments. D) Microbial mat on an asphalt flow. Taken from Jørgensen and  Boetius, 2006.

The deepest bacteria and the deep sea diversity 

Exist different reports of deepest microorganism recovered from this environments, for example Shewanella benthica KT99 was found on sediments on Tonga‐Kermadec Trench, Pacific at 9000 m!. Other reports (Table 1) include the genus Psychromonas sp. CNPT3 from Central North Pacific at 5800m, Shewanella violacea DSS12 located on sediment on Ryukyu Trench, Philippine Sea at 5110 m and other bacterias belonging to Shewanella genus  ⁵. The most abundant microorganism of deeps sea sediments are barophilic and psychrophilic bacteria, such as some members of the Moritella, Colwellia and Shewanella clades. On the hydrothermal vents predominate thermophilic archaeal members of the orders Thermococcales, Methanococcales, Archaeoglobales, Aquificales, and mesophilic and thermophilic bacterial members of Epsilon-proteobacteria have been detected (Zhang 2016).  Microorganism from cool seeps oxidize hydrocarbon compounds by using oxygen or sulphate as the terminal electron acceptor like Methanosarcinales, the dominant anaerobic methanotrophs ⁶and sulphate-reducing bacteria of the Desulfosarcina (Desulfococcus) or Desulfobulbus groups^7,8 however cool seeps microorganism have not been cultivated, representing a new challenge for microbiologist to develop new culture media for recover deep sea bacterias.

An interesting studio determinate the composition for microbial communities of 27 deep-sea surface sediment samples (Figure 2) from all major ocean regions focused on the zone between 1000–5300 m water depth, representative of 70% of the depth distribution of the global deep-sea floor ⁹ . The main conclusion of the study was that deep-sea sediments are inhabited by a core community of few cosmopolitan, abundant bacterial which are affiliated with the JTB255 marine benthic group (class Gammaproteobacteria, order Xanthomonadales) and the OM1 clade (class Actinobacteria, order Acidimicrobiales), where bacterial communities appears to be geographically restricted. Despite the advances, the other 30% of the sediments remains unexplored, especially South America oceans, touching the frontier of knowledge and open a new opportunity to explore the deep sea sediments and bacterial communities associated with different tools as a video-guided in situ analytical instruments and robots to operate and recovering diverse environmental samples.

Figure 2. Community composition of bacterial communities in deep-sea sediment. Taken by Bienhold et al. 2016

Table 1. Different record of microorganism found on deep sea sediments and the depth for each study. Taken from Sieze and Wilson, 2009. 

Biogeochemical cycles and deep sea bacteria

Microorganisms are responsible for 98% of primary production and mediate biogeochemical cycles in the oceans⁴. Bacteria and archaea drive many fundamental processes in marine sediment, including oxidation of organic matter, production of methane and other hydrocarbons, and removal of sulfate from the ocean ¹⁰. For other hand, deep-sea hydrothermal plumes have potential microbial energy sources such as H₂S, Fe, Mn, CH₄, and H₂ ¹¹. These metals are scavenging and oxidate by microorganisms and by binding with organic matter, which is presumably derived from microbial activity ^11,12. The bacterial communities plays important role on carbon cycling due to decomposition of material on the deep-sea bed,  consuming at least 13–30% of the total biological consumption of organic carbon¹³, furthermore, the microorganisms mediate hemosynthetic fixation of carbon ¹¹ and  have different enzymes that break organic material and incorporate it for their metabolism ¹⁴, however, the fluxes of hydrocarbons throughout the water column, the amount of organic material that are accessible to microbial degradation and the timescale of several process where fractions are digested, oxidized and assimilated remain unknown. Future investigation on the relationship between microbial activity and organic matter degradation will provide a better understanding of the impact of this micro world on the deep sea equilibrium, and in situ environmental conditions measurements are necessary for answer this questions. Biogeochemical processes in deep sea sediments can be studied using independent underwater modules that are placed by submersibles and that autonomously measure and record data electronically¹

Adaptation process

The mechanisms by which marine bacteria adapt to different extreme conditions of temperature, pressure and high concentration of certain metals are very inadequately understood, however, some research have determinate that regulated genes,  key for different metabolic process, are responsible for acclimatization in marine bacteria¹⁵. Metatranscriptomic analysis serve as a tool to determinate the gene expression patterns of these microbial groups and their metabolic arsenal for resist hostile conditions. A study revel that deep sea bacteria have a high ratio of rRNA operon copies per genome size, highlighted a high degree of gene regulation to respond rapidly to environmental changes^5,16. Moreover, the deep sea microorganism have the capability to produce several enzymes related to biocatalysts with properties like high salt tolerance, hyperthermostability, barophilicity and cold adaptivity ¹⁷, provide an enormous reservoir of low-temperature and high-pressure adapted enzymes⁵. They also contain a larger repertoire of transport proteins and different proteins that are encoded for chemotaxis, flagellar assembly and motor function to allow them to hunt for dissolved organic matter^18,19. Despite the recent research, several gaps about the functions and the structure of different enzymes exists, for these reasons is imperative the use of Metaproteomic and Metatranscriptomic analysis, and other independent culture proxies to study metabolic mechanisms of deep sea microbial communities.

The unexplored Symbiosis

On nature, symbiosis is the common denominator, however on the deep sea little is known about this phenomenon. An example is the chemolithoautotrophic microorganisms, the primary producers at hydrothermal vents. Diverse animals like mollusks, giant tubeworms, and shrimps depend on the energy flow through these chemoautotrophs, furthermore, the bacterial consortium control rates of redox reactions, modifying the environment and allow that animals to have energy access more easily¹. Other animals like bivalves and tubeworms maintain a symbiosis with chemolithoautotrophic Aquificales and diverse alpha- and gammaproteobacteria²⁰, similarly occurs with deep sea corals, however the symbiotic microbial biosphere remain poorly studied despite bacteria provide several services beneficial to holobiont health, such cycling nutrients, antibiotic production²¹ and the exclusion of pathogens through occupation of available microbial niches ^22,23 maintaining holobiont fitness. A research about bacterial community structure associated with deep-sea corals from the Red Sea stablish that corals exhibited species-specific bacterial associations provide support to the notion that bacteria contribute to environmental adaption of their coral hosts²⁴. It´s necessary study these relationships because the microbial communities on host evolution are fundamental to understand physiological mechanism and the behave of holobiont as a whole.  Technological advances on molecular biology and exploration robots provide new opportunities to address these questions.

References

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