Dissemination and survival of non-indigenous bacterial genomes in pristine Antarctic environments

Comparative genomics reveals the high diversity and adaptation strategies of Polaromonas from polar environments

BACKGROUND

Bacteria from the genus Polaromonas are dominant phylotypes found in a variety of low-temperature environments in polar regions. The diversity and biogeographic distribution of Polaromonas have been largely expanded on the basis of 16 S rRNA gene amplicon sequencing. However, the evolution and cold adaptation mechanisms of Polaromonas from polar regions are poorly understood at the genomic level.

RESULTS

A total of 202 genomes of the genus Polaromonas were analyzed, and 121 different species were delineated on the basis of average nucleotide identity (ANI) and phylogenomic placements. Remarkably, 8 genomes recovered from polar environments clustered into a separate clade ('polar group' hereafter). The genome size, coding density and coding sequences (CDSs) of the polar group were significantly different from those of other nonpolar Polaromonas. Furthermore, the enrichment of genes involved in carbohydrate and peptide metabolism was evident in the polar group. In addition, genes encoding proteins related to betaine synthesis and transport were increased in the genomes from the polar group. Phylogenomic analysis revealed that two different evolutionary scenarios may explain the adaptation of Polaromonas to cold environments in polar regions.

CONCLUSIONS

The global distribution of the genus Polaromonas highlights its strong adaptability in both polar and nonpolar environments. Species delineation significantly expands our understanding of the diversity of the Polaromonas genus on a global scale. In this study, a polar-specific clade was found, which may represent a specific ecotype well adapted to polar environments. Collectively, genomic insight into the metabolic diversity, evolution and adaptation of the genus Polaromonas at the genome level provides a genetic basis for understanding the potential response mechanisms of Polaromonas to global warming in polar regions.

Characterization of Staphylococcus intermedius Group Isolates Associated with Animals from Antarctica and Emended Description of Staphylococcus delphini

Members of the genus Staphylococcus are widespread in nature and occupy a variety of niches, however, staphylococcal colonization of animals in the Antarctic environment has not been adequately studied. Here, we describe the first isolation and characterization of two Staphylococcus intermedius group (SIG) members, Staphylococcus delphini and Staphylococcus pseudintermedius, in Antarctic wildlife. Staphylococcus delphini were found exclusively in Adélie penguins. The report of S. pseudintermedius from Weddell seals confirmed its occurrence in all families of the suborder Caniformia. Partial RNA polymerase beta-subunit (rpoB) gene sequencing, repetitive PCR fingerprinting with the (GTG)5 primer, and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry gave consistent identification results and proved to be suitable for identifying SIG members. Comparative genomics of S. delphini isolates revealed variable genomic elements, including new prophages, a novel phage-inducible chromosomal island, and numerous putative virulence factors. Surface and extracellular protein distribution were compared between genomes and showed strain-specific profiles. The pathogenic potential of S. delphini was enhanced by a novel type of exfoliative toxin, trypsin-like serine protease cluster, and enterotoxin C. Detailed analysis of phenotypic characteristics performed on six Antarctic isolates of S. delphini and eight reference strains from different animal sources enabled us to emend the species description of S. delphini.

Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach

Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities

There is increasing awareness of invasion in microbial communities worldwide, but the mechanisms behind microbial invasions remain poorly understood. Specifically, we know little about how the evolutionary and ecological differences between invaders and natives regulate invasion success and impact. Darwin's naturalization hypothesis suggests that the phylogenetic distance between invaders and natives could be a useful predictor of invasion, and modern coexistence theory proposes that invader-native niche and fitness differences combine to determine invasion outcome. However, the relative importance of phylogenetic distance, niche difference and fitness difference for microbial invasions has rarely been examined. By using laboratory bacterial microcosms as model systems, we experimentally assessed the roles of these differences for the success of bacterial invaders and their impact on native bacterial community structure. We found that the phylogenetic distance between invaders and natives failed to explain invasion success and impact for two of three invaders at the phylogenetic scale considered. Further, we found that invasion success was better explained by invader-native niche differences than relative fitness differences for all three invaders, whereas invasion impact was better explained by invader-native relative fitness differences than niche differences. These findings highlight the utility of considering modern coexistence theory to gain a more mechanistic understanding of microbial invasions.

Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions

Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20°C to -1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle.

Protection of Antarctic microbial communities - 'out of sight, out of mind'

Recent advances in molecular biology techniques have shown the presence of diverse microbial communities and endemic species in Antarctica. Endemic microbes may be a potential source of novel biotechnologically important compounds, including, for example, new antibiotics. Thus, the scientific and biotechnological value of Antarctic terrestrial microbial habitats can be compromised by human visitation to a greater extent than previously realized. The ever-increasing human footprint in Antarctica makes consideration of this topic more pressing, as the number of locations known to be pristine habitats, where increasingly sophisticated cutting-edge research techniques may be used to their full potential, declines. Examination of the Protected Areas system of the Antarctic Treaty shows that microbial habitats are generally poorly protected. No other continent on Earth is dominated to the same degree by microbial species, and real opportunities exist to develop new ways of conceptualizing and implementing conservation of microbial biogeography on a continental scale. Here we highlight potential threats both to the conservation of terrestrial microbial ecosystems, and to future scientific research requiring their study.

Sewage Disposal and Wildlife Health in Antarctica

Sewage and its microbiology, treatment and disposal are important to the topic of Antarctic wildlife health because disposal of untreated sewage effluent into the Antarctic marine environment is both allowed and commonplace. Human sewage contains enteric bacteria as normal flora, and has the potential to contain parasites, bacteria and viruses which may prove pathogenic to Antarctic wildlife. Treatment can reduce levels of micro-organisms in sewage effluent, but is not a requirement of the Environmental Protocol to the Antarctic Treaty (the Madrid Protocol). In contrast, the deliberate release of non-native organisms for any other reason is prohibited. Hence, disposal of sewage effluent to the marine environment is the only activity routinely undertaken in Antarctica knowing that it will likely result in the release of large numbers of potentially non-native species.

When the Madrid Protocol was negotiated, the decision to allow release of untreated sewage effluent was considered the only pragmatic option, as a prohibition would have been costly, and may not have been achievable by many Antarctic operators. In addition, at that time the potential for transmission of pathogens to wildlife from sewage was not emphasised as a significant potential risk. Since then, the transmission of disease-causing agents between species is more widely recognised and it is now timely to consider the risks of continued discharge of sewage effluent in Antarctica and whether there are practical alternatives.