Ex-situ enzyme activity and bacterial community diversity through soil depth profiles in penguin and seal colonies on Vestfold Hills, East Antarctica

Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes

Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.

Abiotic factors influencing soil microbial activity in the northern Antarctic Peninsula region

Microorganisms play a key role in the carbon (C) cycle through soil organic matter (SOM). The rate of SOM mineralization, the influence of abiotic factors on this rate and the potential behaviour of SOM are of particular interest in the northern Antarctic Peninsula and offshore islands. This is one of the most rapidly warming regions on Earth with numerous ice-free areas, some with abundant wildlife and with the greatest known soil organic carbon (SOC) storage in Antarctica. The latter implies extended Antarctic summer conditions promote increased terrestrial plant growth and soil microbial activity (SMA). SMA, determined by respirometry, is a measure of ecosystem function, and depends on microclimatic conditions and soil environmental properties. SMA and the effect of abiotic variables have been analysed in locations with different soil types, on Cierva Point (Antarctic Peninsula), Deception Island and Fildes Peninsula (King George Island). Soil microbial biomass carbon (SMBC) ranged from 5.66 to 196.6 mg SMBC kg^-1and basal respiration (BR) from 2.86 to 160.67 mg CO₂ kg^-1 d^-1. SMBC and BR values were higher in Cierva Point, followed by Fildes Peninsula and Deception Island, showing the same trend of SOM abundance_. Except for Cierva Point, low nitrogen, phosphorus and C concentrations were observed. SMBC/total organic carbon (TOC) levels indicated that SOC was recalcitrant and SOM content was closely related to the extent of vegetation cover observed in situ. High metabolic quotient values obtained at Cierva Point and Deception Island (median values 7.27 and 6.53 mg C-CO₂ g SMBC^-1 h^-1) and low SMBC/TOC in Cierva Point suggest a poor efficiency of the microbial populations in the consumption of the SOC. High SMBC/TOC values obtained in Deception Island indicates that SMBC may influence SOM stabilization. Mineralization rates were very low (negligible values to 1.44%) and sites with the lowest values had the highest SOM.

Selenium volatilization from tundra soils in maritime Antarctica

Maritime Antarctica harbors a large number of penguins and seals that provide considerable input of selenium (Se) originating as guano into terrestrial ecosystems. Subsequent Se emissions via biomethylation and volatilization from these sources of Se have not been studied. Here, penguin colony soils (PCS) and adjacent tundra marsh soils (TMS), seal colony soils (SCS) and adjacent tundra soils (STS), and normal upland tundra soils (NTS) were collected in maritime Antarctica. For the first time, Se volatilization and speciation were investigated in these soils through incubation experiments using chemo-trapping method. The Se contents in PCS, SCS, STS and TMS were highly enriched compared with NTS, with organic matter-bound Se accounting for 70%-80%. Laboratory incubations yielded the greatest Se volatilization rates (VR_Se) in PCS (0.20 ± 0.01 μg kg^-1 d^-1), followed by SCS (0.14 ± 0.01 μg kg^-1 d^-1) at low temperature (4 °C). Soil frozen-thawing induced 1-4 fold increase in VR_Se, and the VR_Se continuously increased until the soils fully thawed. The VR_Se showed a significant positive correlation (R² = 0.96, p < 0.01) with soil temperature. Methylated Se species were dominated by dimethylselenide (DMSe) in PCS and dimethyldiselenide (DMDSe) in SCS. Our results imply that the combination of climate warming, frozen-thawing processes, and high-Se inputs from sea animals will significantly increase tundra soil Se volatilization in maritime Antarctica. High VR_Se from penguin colony soils, and significantly elevated Se levels in the mosses close to penguin colony, suggest that volatilization of Se from penguin colony soils play an important role in the mobilization and regional biogeochemical cycling of Se in maritime Antarctica.

Methyl Chloride and Methyl Bromide Production and Consumption in Coastal Antarctic Tundra Soils Subject to Sea Animal Activities

Methyl chloride (CH₃Cl) and methyl bromide (CH₃Br) are the predominant carriers of natural chlorine and bromine from the troposphere to the stratosphere, which can catalyze the destruction of stratospheric ozone. Here, penguin colony soils (PCS) and the adjacent tundra soils (i.e., penguin-lacking colony soils, PLS), seal colony soils (SCS), tundra marsh soils (TMS), and normal upland tundra soils (UTS) in coastal Antarctica were collected and incubated for the first time to confirm that these soils were CH₃Cl and CH₃Br sources or sinks. Overall, tundra soil acted as a net sink for CH₃Cl and CH₃Br with potential flux ranges from -18.1 to -2.8 pmol g^-1 d^-1 and -1.32 to -0.24 pmol g^-1 d^-1, respectively. The deposition of penguin guano or seal excrement into tundra soils facilitated the simultaneous production of CH₃Cl and CH₃Br and resulted in a smaller sink in PCS, SCS, and PLS. Laboratory-based thermal treatments and anaerobic incubation experiments suggested that the consumption of CH₃Cl and CH₃Br was predominantly mediated by microbes while the production was abiotic and O₂ independent. Temperature gradient incubations revealed that increasing soil temperature promoted the consumption of CH₃Cl and CH₃Br in UTS, suggesting that the regional sink may increase with Antarctic warming, depending on changes in soil moisture and abiotic production rates.

Effects of Sea Animal Activities on Tundra Soil Denitrification and nirS- and nirK-Encoding Denitrifier Community in Maritime Antarctica

In maritime Antarctica, sea animals, such as penguins or seals, provide a large amount of external nitrogen input into tundra soils, which greatly impact nitrogen cycle in tundra ecosystems. Denitrification, which is closely related with the denitrifiers, is a key step in nitrogen cycle. However, effects of sea animal activities on tundra soil denitrification and denitrifier community structures still have received little attention. Here, the abundance, activity, and diversity of nirS- and nirK-encoding denitrifiers were investigated in penguin and seal colonies, and animal-lacking tundra in maritime Antarctica. Sea animal activities increased the abundances of nirS and nirK genes, and the abundances of nirS genes were significantly higher than those of nirK genes (p < 0.05) in all tundra soils. Soil denitrification rates were significantly higher (p < 0.05) in animal colonies than in animal-lacking tundra, and they were significantly positively correlated (p < 0.05) with nirS gene abundances instead of nirK gene abundances, indicating that nirS-encoding denitrifiers dominated the denitrification in tundra soils. The diversity of nirS-encoding denitrifiers was higher in animal colonies than in animal-lacking tundra, but the diversity of nirK-encoding denitrifiers was lower. Both the compositions of nirS- and nirK-encoding denitrifiers were similar in penguin or seal colony soils. Canonical correspondence analysis indicated that the community structures of nirS- and nirK-encoding denitrifiers were closely related to tundra soil biogeochemical processes associated with penguin or seal activities: the supply of nitrate and ammonium from penguin guano or seal excreta, and low C:N ratios. In addition, the animal activity-induced vegetation presence or absence had an important effect on tundra soil denitrifier activities and nirK-encoding denitrifier diversities. This study significantly enhanced our understanding of the compositions and dynamics of denitrifier community in tundra ecosystems of maritime Antarctica.

Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird

Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.

Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances

Both Bacteria and Archaea are important players in soil biogeochemical cycles. Both chromium (Cr) and perfluoroalkyl substances (PFASs) are widely present in soil environment. However, the depth-related distribution of microbial community in soils contaminated by Cr or/and PFASs remains unknown. Hence, the present study applied quantitative PCR assay and Illumina MiSeq sequencing to investigate the vertical variations of archaeal and bacterial communities in soils (0.5-12.5m depth) contaminated by chrome plating waste and the potential effects of Cr and PFASs. Both bacterial and archaeal communities displayed the remarkable depth-related changes of abundance (2.16×10⁷-5.05×10⁹ and 4.95×10⁵-2.56×10⁸ 16S rRNA gene copies per gram dry soil respectively for Bacteria and Archaea), diversity (bacterial and archaeal Shannon diversity indices of 5.06-6.34 and 2.91-4.61, respectively) and structure. However, at each soil depth, bacterial community had higher abundance, richness and diversity than archaeal community. Soil bacterial communities were mainly composed of Proteobacteria, Chloroflexi, Actinobacteria and Firmicutes, and archaeal communities were dominated by Thaumarchaeota and unclassified Archaea. Moreover, microbial abundance and richness increased with increasing perfluorohexane sulfonate (PFHxS) content. Microbial abundance was correlated to total Cr, and archaeal richness was correlated to total Cr and Cr(IV). In addition, total Cr might be a key determinant of soil microbial community structure.

Leaching of mercury from seal carcasses into Antarctic soils

More than 400 seal mummies and skeletons are now mapped in the northern part of James Ross Island, Antarctica. Decomposing carcasses represent a rare source of both organic matter and associated elements for the soil. Owing to their high trophic position, seals are known to carry a significant mercury body burden. This work focuses on the extent of the mercury input from seal carcasses and shows that such carcasses represent locally significant sources of mercury and methylmercury for the environment. Mercury contents in soil samples from the surrounding areas were determined using a single-purpose AAS mercury analyzer. For the determination of methylmercury, an ultra-sensitive isotopic dilution HPLC-ICP-MS technique was used. In the soils lying directly under seal carcasses, mercury contents were higher, with levels reaching almost 40 μg/kg dry weight of which methylmercury formed up to 2.8 % of the total. The spatial distribution implies rather slow vertical transport to the lower soil layers instead of a horizontal spread. For comparison, the background level of mercury in soils of the investigated area was found to be 8 μg/kg dry weight, with methylmercury accounting for less than 0.1 %. Apart from the direct mercury input, an enhanced level of nutrients in the vicinity of carcasses enables the growth of lichens and mosses with accumulative ability with respect to metals. The enhanced capacity of soil to retain mercury is also anticipated due to the high content of total organic carbon (from 1.6 to 7.5 %). According to the results, seal remains represent a clear source of mercury in the observed area.

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile

Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p < 0.01); this indicated that historical penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800–2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400–1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today.

Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing

This study assessed the diversity and composition of bacterial communities in four different soils (human-, penguin-, seal-colony impacted soils and pristine soil) in the Fildes Region (King George Island, Antarctica) using 454 pyrosequencing with bacterial-specific primers targeting the 16S rRNA gene. Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia were abundant phyla in almost all the soil samples. The four types of soils were significantly different in geochemical properties and bacterial community structure. Thermotogae, Cyanobacteria, Fibrobacteres, Deinococcus-Thermus, and Chlorobi obviously varied in their abundance among the 4 soil types. Considering all the samples together, members of the genera Gaiella, Chloracidobacterium, Nitrospira, Polaromonas, Gemmatimonas, Sphingomonas, and Chthoniobacter were found to predominate, whereas members of the genera Chamaesiphon, Herbaspirillum, Hirschia, Nevskia, Nitrosococcus, Rhodococcus, Rhodomicrobium, and Xanthomonas varied obviously in their abundance among the four soil types. Distance-based redundancy analysis revealed that pH (p < 0.01), phosphate phosphorus (p < 0.01), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the community distribution of soil bacteria. To our knowledge, this is the first study to explore the soil bacterial communities in human-, penguin-, and seal- colony impacted soils from ice-free areas in maritime Antarctica using high-throughput pyrosequencing.