Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics

Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.

Comparing resistome profiles from anthropogenically impacted and non-impacted areas of two South Shetland Islands - Maritime Antarctica

Whalers Bay, in Deception Island, has one of the most anthropogenically impacted areas in Maritime Antarctica. However, considering the volcanic nature (high concentrations of heavy metals) of Deception Island's soils, this putative anthropogenic impact should be carefully investigated. In this context, the objective of this study was to compare resistome profiles of impacted and non-impacted areas in Deception Island (Whalers Bay, Crater Lake, and Fumarole Bay) and Livingston Island (Hannah Point) in order to investigate the microbiome tolerance/resistance mechanisms selected as a function of environmental drivers. Metagenomics was used to search for genes conferring resistance/tolerance to antibiotics, biocides, and heavy metals. Whalers Bay has a greater diversity of antibiotic, biocide, and heavy metal resistance classes found in its microbiomes. However, Hannah Point, at Livingston Island, has a greater abundance of antibiotic and biocide resistance/tolerance genes. The microbiome of Deception Island's non-impacted areas (Crater Lake and Fumarole Bay) showed resistance/tolerance genes almost entirely to heavy metals. Pb was found in higher concentrations in Whalers Bay soil in comparison to the other areas, indicating human contamination. The non-metric multidimensional scaling (NMDS) analysis revealed that Pb concentrations influenced resistome profiles in Whalers Bay soil. Despite the effect of Pb on the microbial communities of Whalers Bay, most heavy metal concentrations did not have a significant impact on resistome genes, suggesting that the volcanic soil heavy metal concentration of Deception Island has little biological influence.

Dynamics of microbial stress responses driven by abiotic changes along a temporal gradient in Deception Island, Maritime Antarctica

Whalers Bay (WB), Deception Island, is an environment that can drastically change its temperature within a few meters. The main forms of life inhabiting this environment are microorganisms, which, due to the high diversity and their adaptive potential, can survive and thrive under harsh stress conditions. However, the genetic potential and mechanisms to cope with fluctuating adverse conditions as well as what extent environmental variations shape the microbial community over the years it is still unknown in Antarctic environments. In this work, sediments collected in a transect in Whalers Bay, Deception Island, during the Austral Summers of 2014, 2015 and 2017 were analyzed using shotgun metagenomics. Sequence data were further processed with the SqueezeMeta tool for assembly, gene prediction, mapping, taxonomic and functional annotations. Results showed that stress-related functions had the influence of temperatures and solar radiation observed in the years of 2015 and 2017. The most differentiated functions were the ones related to oxidative stress, comparing 2014 vs 2015 and 2014 vs 2017. The genes coding for HSP20 and oxidoreductases (nrdH, grxA, korC and korD), as well as the genes clpE, cspL, and operons mtrAB and vicKR, were differentially enriched between the years, most of them found in gram-positive bacteria. The selective pressures of temperature and radiation may have favored the growth of gram-positive bacteria in 2017, with emphasis on Arthrobacter genus. Data gathered in this work showed that temperature and solar radiation could potentially be the primary driving forces shaping the repertoire of stress-response genes for the maintenance of microbial diversity in WB Antarctic sediments.

Unveiling resistome profiles in the sediments of an Antarctic volcanic island

The Deception Island, located in Maritime Antarctica, is a volcanic island with geothermal activity and one of the most visited by tourists. However, the extent of the anthropogenic impact remains largely unknown and the factors shaping the resistance/tolerance mechanisms in the microbiomes from Whalers Bay ecosystems have never been investigated. In this context, this study aimed to reveal the resistome profiles of Whalers Bay sediments and correlate them with environmental factors. Samples were collected at four sites during the summer 2014/2015 along a transect of 27.5 m in the Whalers Bay sediments. DNA isolated from sediment samples was sequenced using the Illumina HiSeq platform. Bioinformatic analyses allowed the assembly of contigs and scaffolds, prediction of ORFs, and taxonomic and functional annotation using NCBI RefSeq database and KEGG orthology, respectively. Microorganisms belonging to the genera Psychrobacter, Flavobacterium and Polaromonas were shown to dominate all sites, representing 60% of taxonomic annotation. Arsenic (As), copper (Cu) and iron (Fe) were the most abundant metal resistance/tolerance types found in the microbiomes. Beta-lactam was the most common class related to antibiotics resistance/tolerance, corroborating with previous environmental resistome studies. The acridine class was the most abundant amongst the biocide resistance/tolerances, related to antiseptic compounds. Results gathered in this study reveal a repertoire of resistance/tolerance classes to antibiotics and biocides unusually found in Antarctica. However, given the volcanic nature (heavy metals-rich region) of Deception Island soils, this putative impact must be viewed with caution.

Laundry wastewater and domestic sewage pilot-scale anaerobic treatment: Microbial community resilience regarding sulfide production

In this study, the removal of anionic surfactant Linear Alkylbenzene Sulfonate (LAS) from laundry wastewater was evaluated in co-digestion with domestic sewage, using a pilot-scale Expanded Granular Sludge Bed reactor. Surfactant influent concentration was enhanced from 5 ± 3 mg LAS L^-1 (stage I) to 19 ± 10 mg LAS L^-1 (stage II) and 36 ± 19 mg LAS L^-1 (stage III) throughout reactor operation. Sulfide levels higher than 20 mg L^-1 influenced LAS removal efficiency, which decreased from 71% to 55% and 32% in stage I, II and III, respectively. Acclimation of microbial population was verified and higher relative abundance of the genera similar to Cytophaga, Bacteroides, Syntrophus and Syntrophobacter in the early stages (adaptation and stage I) was replaced by higher relative abundance of the genera Anaerophaga, Nitrosovibrio, Sulfurovum and Desulfovibrio in the last stages (stage II and III).