The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review

Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.

Deciphering the evolvement of microbial communities from hydrothermal vent sediments in a global change perspective

Microbial communities first respond to changes of external environmental conditions. Observing the microbial responses to environmental changes in terms of taxonomic and functional biodiversity is therefore of great interest, particularly in extreme environments, where the already extreme conditions can become even harsher. In this study, sediment samples from three different shallow hydrothermal vents in Levante Bay (Vulcano Island, Aeolian Islands, Italy) were used to set up microcosm experiments with the aim to explore the microbial dynamics under changing conditions of pH and redox potential over a 90-days period. The leading hypothesis was to establish under microcosm conditions whether the starting microbial communities of the sediments evolved differently depending on their origin. To profile the dynamics of microbial populations over time, biodiversity, enzymatic profile, total cell abundance estimations, total/respiring cell ratio were estimated by using different approaches. An evident change in the microbial community structure was observed, mainly in the microcosm containing the sediment from the most acidified site, which was characterized by a highly diversified microbial community (in prevalence composed of Thermotoga, Desulfobacterota, Planctomycetota, Synergistota and Deferribacterota). An increase in microbial resistant forms (e.g., spore-forming species) with anaerobic metabolism was detected in all experimental conditions. Differential physiological responses characterized the sedimentary microbial communities. Proteolytic activity appeared to be stimulated under microcosm conditions, whereas the alkaline phosphatase activity was significantly depressed at low pH values, like those that were measured at the station showing intermediate pH-conditions. The results confirmed a differential response of microbial communities depending on the starting environmental conditions.

Hyperthermophile diversity microbes in the Calientes geothermal field, Tacna, Peru

Hyperthermophile microorganisms have been discovered worldwide, and several studies regarding biodiversity and the potential biotechnological applications have been reported. In this work, we describe for the first time the diversity of hyperthermophile communities in the Calientes Geothermal Field (CGF) located 4400 m above sea level in Tacna Region, Perú. Three hot springs were monitored and showed a temperature around 84 to 88 °C, for the microbiome analyzed was taken by sampling of sediment and water (pH 7.3-7.6). The hyperthermophile diversity was determined by PCR, DGGE, and DNA sequencing. The sediments analyzed showed a greater diversity than water samples. Sediments showed a more abundant population of bacteria than archaea, with the presence of at least 9 and 5 phylotypes, respectively. Most interestingly, in some taxa of bacteria (Bacillus) and archaea (Haloarcula and Halalkalicoccus), any of operational taxonomic units (OTUs) have not been observed before in hyperthermophile environments. Our results provide insight in the hyperthermophile diversity and reveal the possibility to develop new biotechnological applications based on the kind of environments.

Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field

Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.

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

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.

Ecological and Biotechnological Relevance of Mediterranean Hydrothermal Vent Systems

Marine hydrothermal systems are a special kind of extreme environments associated with submarine volcanic activity and characterized by harsh chemo-physical conditions, in terms of hot temperature, high concentrations of CO2 and H2S, and low pH. Such conditions strongly impact the living organisms, which have to develop adaptation strategies to survive. Hydrothermal systems have attracted the interest of researchers due to their enormous ecological and biotechnological relevance. From ecological perspective, these acidified habitats are useful natural laboratories to predict the effects of global environmental changes, such as ocean acidification at ecosystem level, through the observation of the marine organism responses to environmental extremes. In addition, hydrothermal vents are known as optimal sources for isolation of thermophilic and hyperthermophilic microbes, with biotechnological potential. This double aspect is the focus of this review, which aims at providing a picture of the ecological features of the main Mediterranean hydrothermal vents. The physiological responses, abundance, and distribution of biotic components are elucidated, by focusing on the necto-benthic fauna and prokaryotic communities recognized to possess pivotal role in the marine ecosystem dynamics and as indicator species. The scientific interest in hydrothermal vents will be also reviewed by pointing out their relevance as source of bioactive molecules.

Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments

Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla, including endospore-forming Bacilli and candidate phylum Marinisomatota. One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies, seven extracellular CAZymes, six polysaccharide lyases, and multiple sugar transporters. This population has the potential to degrade a broad spectrum of polysaccharides including chitin, cellulose, pectin, alginate, chondroitin, and carrageenan. We also describe thermophiles affiliating with the genera Thermosyntropha, Thermovirga, and Kosmotoga with the capability to make a living on nucleic acids, lipids, or multiple macromolecule classes, respectively. Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g., MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g., MAGs affiliating with Thermodesulfobacterium or Desulforudaceae). The growth of methanogens or the production of methane was not observed in any condition, indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments. We provide new insights into the niches, and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic, sulfate-reducing, and fermentative thermophilic conditions. These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems.

A Proposed Geobiology-Driven Nomenclature for Astrobiological In Situ Observations and Sample Analyses

As the exploration of Mars and other worlds for signs of life has increased, the need for a common nomenclature and consensus has become significantly important for proper identification of nonterrestrial/non-Earth biology, biogenic structures, and chemical processes generated from biological processes. The fact that Earth is our single data point for all life, diversity, and evolution means that there is an inherent bias toward life as we know it through our own planet's history. The search for life "as we don't know it" then brings this bias forward to decision-making regarding mission instruments and payloads. Understandably, this leads to several top-level scientific, theoretical, and philosophical questions regarding the definition of life and what it means for future life detection missions. How can we decide on how and where to detect known and unknown signs of life with a single biased data point? What features could act as universal biosignatures that support Darwinian evolution in the geological context of nonterrestrial time lines? The purpose of this article is to generate an improved nomenclature for terrestrial features that have mineral/microbial interactions within structures and to confirm which features can only exist from life (biotic), features that are modified by biological processes (biogenic), features that life does not affect (abiotic), and properties that can exist or not regardless of the presence of biology (abiogenic). These four categories are critical in understanding and deciphering future returned samples from Mars, signs of potential extinct/ancient and extant life on Mars, and in situ analyses from ocean worlds to distinguish and separate what physical structures and chemical patterns are due to life and which are not. Moreover, we discuss hypothetical detection and preservation environments for extant and extinct life, respectively. These proposed environments will take into account independent active and ancient in situ detection prospects by using previous planetary exploration studies and discuss the geobiological implications within an astrobiological context.

A Special Issue on Microorganisms from Extreme Environments in Memory of Luigi Michaud (1974–2014)

A special issue (SI) titled “Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives” has been launched with the aim of showcasing the diversity and biotechnological potential of extremophilic microorganisms. The issue includes 10 research papers and four reviews that mainly address prokaryotes inhabiting hyperarid, hypercold, hyperalkaline and hypersaline (or polyextreme) environments, spanning from deserts to meromictic and glacier lakes around the globe. Thermophilic prokaryotes from shallow hydrothermal vents and Antarctic geothermal soils are also treated. The ecology and biotechnological perspectives of eukaryotes are discussed in two review papers and one research paper. This special issue serves as a memorial to Dr. Luigi Michaud (1974–2014), who dramatically passed away in Antarctica during underwater sampling activities.