Hydrolytic enzyme-producing microbes in the Antarctic oligochaete Grania sp. (Annelida)

Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome

The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.

Trophic Position of the White Worm (Enchytraeus albidus) in the Context of Digestive Enzyme Genes Revealed by Transcriptomics Analysis

To assess the impact of Enchytraeidae (potworms) on the functioning of the decomposer system, knowledge of the feeding preferences of enchytraeid species is required. Different food preferences can be explained by variations in enzymatic activities among different enchytraeid species, as there are no significant differences in the morphology or anatomy of their alimentary tracts. However, it is crucial to distinguish between the contribution of microbial enzymes and the animal's digestive capacity. Here, we computationally analyzed the endogenous digestive enzyme genes in Enchytraeus albidus. The analysis was based on RNA-Seq of COI-monohaplotype culture (PL-A strain) specimens, utilizing transcriptome profiling to determine the trophic position of the species. We also corroborated the results obtained using transcriptomics data from genetically heterogeneous freeze-tolerant strains. Our results revealed that E. albidus expresses a wide range of glycosidases, including GH9 cellulases and a specific digestive SH3b-domain-containing i-type lysozyme, previously described in the earthworm Eisenia andrei. Therefore, E. albidus combines traits of both primary decomposers (primary saprophytophages) and secondary decomposers (sapro-microphytophages/microbivores) and can be defined as an intermediate decomposer. Based on assemblies of publicly available RNA-Seq reads, we found close homologs for these cellulases and i-type lysozymes in various clitellate taxa, including Crassiclitellata and Enchytraeidae.

Diversity and enzymatic, biosurfactant and phytotoxic activities of culturable Ascomycota fungi present in marine sediments obtained near the South Shetland Islands, maritime Antarctica

We studied the culturable fungal community recovered from deep marine sediments in the maritime Antarctic, and assessed their capabilities to produce exoenzymes, emulsifiers and metabolites with phytotoxic activity. Sixty-eight Ascomycota fungal isolates were recovered and identified. The most abundant taxon recovered was the yeast Meyerozyma guilliermondii, followed by the filamentous fungi Penicillium chrysogenum, P. cf. palitans, Pseudeurotium cf. bakeri, Thelebolus balaustiformis, Antarctomyces psychrotrophicus and Cladosporium sp. Diversity indices displayed low values overall, with the highest values obtained at shallow depth, decreasing to the deepest location sampled. Only M. guilliermondii and P. cf. palitans were detected in the sediments at all depths sampled, and were the most abundant taxa at all sample sites. The most abundant enzymes detected were proteases, followed by invertases, cellulases, lipases, carrageenases, agarases, pectinases and esterases. Four isolates showed good biosurfactant activity, particularly the endemic species A. psychrotrophicus. Twenty-four isolates of P. cf. palitans displayed strong phytotoxic activities against the models Lactuca sativa and Allium schoenoprasum. The cultivable fungi recovered demonstrated good biosynthetic activity in the production of hydrolytic exoenzymes, biosurfactant molecules and metabolites with phytotoxic activity, reinforcing the importance of documenting the taxonomic, ecological and biotechnological properties of fungi present in deep oceanic sediments of the Southern Ocean.

Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean

Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.

Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules

Microbe–invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate–bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.

Antarctic Porifera homogenates as a source of enzymes and antibacterial substances: first results

Marine Porifera (sponges) are known to produce several bioactive metabolites having a biotechnological potential, mostly derived from their bacterial symbionts; however, current knowledge on the production of metabolites such as enzymes and antibacterial molecules in sponges living in Antarctic environments is not fully exhaustive and needs further deepened investigation. The interest in discovering the broad spectrum of natural products potentially derived from species adapted to colonize extreme environments stimulates the research toward Antarctic sponge bioprospection. In this study, whole homogenates of Antarctic Demospongiae, belonging to five different species [Haliclona (Rhizoniera) sp., Haliclona (Rhizoniera) dancoi, Microxina sarai, Dendrilla antarctica, and Mycale acerata] were collected from Terra Nova Bay (Ross Sea) and examined for presence and activity of enzymes, including lysozyme, and antibacterial substances. Enzyme activities (leucine aminopeptidase, beta-glucosidase, and alkaline phosphatase) were measured using fluorogenic substrates; lysozyme content was determined on plates containing lyophilized Micrococcus lysodeikticus cell walls as a substrate. Homogenates were screened in microtiter plates for their antibacterial activity against Antarctic bacterial isolates, and the absorbance reduction was measured with a microplate reader. All homogenates exhibited proteolytic, glycolytic, and phosphatasic activities, lysozyme and antibacterial activities at near “in situ” temperature (5 °C), with some differences among the examined species. Results confirmed that Antarctic sponge homogenates are interesting sources of different bioactive substances, likely produced from associated bacterial symbionts, and that could have great potential to be used in medicine or industrial applications.

The Variety and Inscrutability of Polar Environments as a Resource of Biotechnologically Relevant Molecules

The application of an ever-increasing number of methodological approaches and tools is positively contributing to the development and yield of bioprospecting procedures. In this context, cold-adapted bacteria from polar environments are becoming more and more intriguing as valuable sources of novel biomolecules, with peculiar properties to be exploited in a number of biotechnological fields. This review aims at highlighting the biotechnological potentialities of bacteria from Arctic and Antarctic habitats, both biotic and abiotic. In addition to cold-enzymes, which have been intensively analysed, relevance is given to recent advances in the search for less investigated biomolecules, such as biosurfactants, exopolysaccharides and antibiotics.

Validating biochemical features at the genome level in the Antarctic bacterium Hymenobacter sp. strain UV11

We present experimental data that complement and validate some biochemical features at the genome level in the UVC-resistant Antarctic bacterium Hymenobacter sp. UV11 strain. The genome was sequenced, assembled and annotated. It has 6 096 246 bp, a GC content of 60.6% and 5155 predicted genes. The secretome analysis, by combining in silico predictions with shotgun proteomics data, showed that UV11 strain produces extracellular proteases and carbohydrases with potential biotechnological uses. We observed the formation of outer membrane vesicles, mesosomes and carbon-storage compounds by using transmission electron microscopy. The in silico analysis of the genome revealed the presence of genes involved in the metabolism of glycogen-like molecules and starch. By HPLC-UV-Vis analysis and 1H-NMR spectra, we verified that strain UV11 produces xanthophyll-like carotenoids such as 2'-hydroxyflexixanthin, and the in silico analysis showed that this bacterium has genes involved in the biosynthesis of cathaxanthin, zeaxanthin and astaxanthin. We also found genes involved in the repair of UV-damaged DNA such as a photolyase, the nucleotide excision repair system and the production of ATP-dependent proteases that are important cellular components involved in the endurance to physiological stresses. This information will help us to better understand the ecological role played by Hymenobacter strains in the extreme Antarctic environment.

A Review on the Use of Microalgae for Sustainable Aquaculture

Traditional aquaculture provides food for humans, but produces a large amount of wastewater, threatening global sustainability. The antibiotics abuse and the water replacement or treatment causes safety problems and increases the aquaculture cost. To overcome environmental and economic problems in the aquaculture industry, a lot of efforts have been devoted into the application of microalgae for wastewater remediation, biomass production, and water quality control. In this review, the systematic description of the technologies required for microalgae-assisted aquaculture and the recent progress were discussed. It deeply reviews the problems caused by the discharge of aquaculture wastewater and introduces the principles of microalgae-assisted aquaculture. Some interesting aspects, including nutrients assimilation mechanisms, algae cultivation systems (raceway pond and revolving algal biofilm), wastewater pretreatment, algal-bacterial cooperation, harvesting technologies (fungi-assisted harvesting and flotation), selection of algal species, and exploitation of value-added microalgae as aquaculture feed, were reviewed in this work. In view of the limitations of recent studies, to further reduce the negative effects of aquaculture wastewater on global sustainability, the future directions of microalgae-assisted aquaculture for industrial applications were suggested.

Characterization of the cellulase-secretome produced by the Antarctic bacterium Flavobacterium sp. AUG42

Flavobacterium sp. AUG42 is a cellulase-producing bacterium isolated from the Antarctic oligochaete Grania sp. (Annelida). In this work, we report that AUG42 produces a glycoside hydrolase cocktail with CMCase, PASCase and cellobiase activities (optimum pHs and temperatures ranging from 5.5 to 6.5 and 40 to 50 °C, respectively). The time-course analyses of the bacterial growth and cellulase production showed that the cocktail has maximal activity at the stationary phase when growing at 16 °C with filter paper as a cellulosic carbon source, among the tested substrates. The analyses of the CAZome and the identification of secreted proteins by shotgun Mass Spectrometry analysis showed that five glycoside hydrolyses are present in the bacterial secretome, which probably cooperate in the degradation of the cellulosic substrates. Two of these glycoside hydrolyses may harbor putative carbohydrate binding modules, both with a cleft-like active site. The cellulolytic cocktail was assayed in saccharification experiments using carboxymethylcellulose as a substrate and results showed the release of glucose (a fermentable sugar) and other reducing-sugars, after 24 h incubation. The ecological relevance of producing cellulases in the Antarctic environment, as well as their potential use in the bio-refinery industry, are discussed.

Bacteria Associated with Marine Benthic Invertebrates from Polar Environments: Unexplored Frontiers for Biodiscovery?

The ecological function of bacteria-invertebrate interactions in Polar areas remains poorly understood, despite increasing evidence that microbial metabolites may play pivotal roles in host-associated chemical defense and in shaping the symbiotic community structure. The metabolic and physiological changes that these organisms undergo in response to adapting to extreme conditions result in the production of structurally and functionally novel biologically active molecules. Deepening our knowledge on the interactions between bacteria and their invertebrate host would be highly helpful in providing the rationale for why (e.g., competition or cooperative purpose) and which (whether secondary metabolites, enzymes, or proteins) bioactive compounds are produced. To date, cold-adapted bacteria associated with marine invertebrates from the Arctic and Antarctica have not been given the attention they deserve and the versatility of their natural products remains virtually unexplored, even if they could represent a new attractive frontier in the search for novel natural compounds. This review is aimed at showcasing the diversity of cold-adapted bacteria associated with benthic invertebrates from Polar marine areas, highlighting the yet unexplored treasure they represent for biodiscovery.

Agarolytic culturable bacteria associated with three antarctic subtidal macroalgae

Bacterial communities of Antarctic marine macroalgae remain largely underexplored in terms of diversity and biotechnological applications. In this study, three Antarctic subtidal macroalgae (Himantothallus grandifolius, Pantoneura plocamioides and Plocamium cartilagineum), two of them endemic of Antarctica, were investigated as a source for isolation of agar-degrading bacteria. A total of 21 epiphytic isolates showed agarolytic activity at low temperature on agar plates containing agar as the sole carbon source. 16S rRNA identification showed that the agar-degrading bacteria belonged to the genera Cellulophaga, Colwellia, Lacinutrix, Olleya, Paraglaciecola, Pseudoalteromonas and Winogradskyella. The agarase enzyme from a potential new species of the genus Olleya was selected for further purification. The enzyme was purified from the culture supernatant of Olleya sp. HG G5.3 by ammonium sulfate precipitation and ion-exchange chromatography. Molecular weight of the agarase was estimated to be 38 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The purified enzyme exhibited activity at 4 °C, retaining > 50% of its maximum activity at this temperature. This is the first study reporting the phylogeny of agar-degrading bacteria isolated from Antarctic subtidal macroalgae and the results suggest the huge potential of Antarctic algae-associated bacteria as a source of cold-active hydrolytic enzymes of biotechnological interest.