Distribution and diversity of soil microfauna from East Antarctica: assessing the link between biotic and abiotic factors

Population growth of two limno-terrestrial Antarctic microinvertebrates in different aqueous soil media

Terrestrial microinvertebrates provide important carbon and nutrient cycling roles in soil environments, particularly in Antarctica where larger macroinvertebrates are absent. The environmental preferences and ecology of rotifers and tardigrades in terrestrial environments, including in Antarctica, are not as well understood as their temperate aquatic counterparts. Developing laboratory cultures is critical to provide adequate numbers of individuals for controlled laboratory experimentation. In this study, we explore aspects of optimising laboratory culturing for two terrestrially sourced Antarctic microinvertebrates, a rotifer (Habrotrocha sp.) and a tardigrade (Acutuncus antarcticus). We tested a soil elutriate and a balanced salt solution (BSS) to determine their suitability as culturing media. Substantial population growth of rotifers and tardigrades was observed in both media, with mean rotifer population size increasing from 5 to 448 ± 95 (soil elutriate) and 274 ± 78 (BSS) individuals over 60 days and mean tardigrade population size increasing from 5 to 187 ± 65 (soil elutriate) and 138 ± 37 (BSS) over 160 days. We also tested for optimal dilution of soil elutriate in rotifer cultures, with 20-80% dilutions producing the largest population growth with the least variation in the 40% dilution after 36 days. Culturing methods developed in this study are recommended for use with Antarctica microinvertebrates and may be suitable for similar limno-terrestrial microinvertebrates from other regions.

Biogeographic survey of soil bacterial communities across Antarctica

BACKGROUND

Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.

RESULTS

Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.

CONCLUSIONS

Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.

The use of different 16S rRNA gene variable regions in biogeographical studies

16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.

Assessing risks from fuel contamination in Antarctica: Dynamics of diesel ageing in soil and toxicity to an endemic nematode

Fuel spills are a major source of contamination in terrestrial environments in Antarctica. Little is known of the effects of hydrocarbon contaminants in fuels on Antarctic terrestrial biota, and how these change as fuel ages within soil. In this study we investigate the sensitivity of juveniles of the endemic Antarctic nematode Plectus murrayi to diesel-spiked soil. Toxicity tests were conducted on soil elutriates, and changes in concentrations of hydrocarbons, polar compounds and PAHs were assessed as the spiked soil was artificially aged at 3 °C over a 45-week period, representing multiple summer seasons of fuel degradation. Nematodes were most sensitive to elutriates made from freshly spiked soils (LC50 419 μg/L TPH and 156 μg/L TPH-SG), with a subsequent decline in toxicity observed in the first 6 weeks of laboratory ageing (LC50 2945 μg/L TPH and 694 μg/L TPH-SG). Effects were still evident up to 45 weeks (lowest observed effect concentration 2123 μg/L TPH) despite hydrocarbons being depleted from soils with ageing (84 % loss) and elutriates becoming dominated by polar metabolites (95 % polar). Nematode sensitivity throughout the ageing period showed evidence of a relationship between LC50 and the proportions of the lighter carbon range fraction of TPH in elutriates, the F2 fraction (C_10-14). This study is the first to estimate the sensitivity of Antarctic terrestrial fauna to diesel and provides novel data on the dynamics of fuel chemistry under Antarctic conditions and how this influences toxicity. Findings contribute to predicting ecological risk at existing diesel fuel spill sites in Antarctica, to the derivation of site-specific remediation targets, and to environmental guidelines to assess ecosystem health.

Phagotrophic protists (protozoa) in Antarctic terrestrial ecosystems: diversity, distribution, ecology, and best research practices

Phagotrophic protists (formerly protozoa) are a highly diverse, polyphyletic grouping of generally unicellular, heterotrophic eukaryotes that are key regulators of the soil microbiome. The biodiversity and ecology of soil phagotrophic protists are still largely uncharacterized, especially in the Antarctic, which possesses some of the harshest terrestrial environments known and potentially many physiologically unique and scientifically interesting species. Antarctic soil systems are also highly limited in terms of moisture, temperature, and carbon, and the resulting reduced biological complexity can facilitate fine-tuned investigation of the drivers and functioning of microbial communities. To facilitate and encourage future research into protist biodiversity and ecology, especially in context of the broader functioning of Antarctic terrestrial communities, I review the biodiversity, distribution, and ecology of Antarctic soil phagotrophic protists. Biodiversity appears to be highly structured by region and taxonomic group, with the Antarctic Peninsula having the highest taxonomic diversity and ciliates (Ciliophora) being the most diverse taxonomic group. However, richness estimates are likely skewed by disproportionate sampling (over half of the studies are from the peninsula), habitat type bias (predominately moss-associated soils), investigator bias (toward ciliates and the testate amoeba morphogroup), and methodological approach (toward cultivation and morphological identification). To remedy these biases, a standardized methodology using both morphological and molecular identification and increased emphasis on microflagellate and naked amoeba morphogroups is needed. Additionally, future research should transition away from biodiversity survey studies to dedicated ecological studies that emphasize the function, ecophysiology, endemicity, dispersal, and impact of abiotic drivers beyond moisture and temperature.

Sensitivity to Copper and Development of Culturing and Toxicity Test Procedures for the Antarctic Terrestrial Nematode Plectus murrayi

Environmental quality guideline values and remediation targets, specific to Antarctic ecosystems, are required for the risk assessment and remediation of contaminated sites in Antarctica. Ecotoxicological testing with Antarctic soil organisms is fundamental in determining reliable contaminant effect threshold concentrations. The present study describes the development of optimal culturing techniques and aqueous toxicity test procedures for an endemic Antarctic soil nematode, Plectus murrayi, which lives within interstitial waters between soil particles. Toxicity tests were of extended duration to account for the species' physiology and life-history characteristics. Plectus murrayi was sensitive to aqueous copper with a 50% effective concentration for egg-hatching success of 139 µg/L. Hatched juveniles that were first exposed to copper as eggs appeared to be less sensitive than those first exposed at the hatched J2 stage, indicating a potential protective effect of the egg. Sensitivity of juveniles to copper increased with exposure duration, with 50% lethal concentrations of 478 and 117 µg/L at 21 and 28 d, respectively. The present study describes new methods for the application of an environmentally relevant test species to the risk assessment of contaminants in Antarctic soil and provides the first estimates of sensitivity to a toxicant for an Antarctic terrestrial microinvertebrate. Environ Toxicol Chem 2020;39:482-491. © 2019 SETAC.

Diversity and feeding strategies of soil microfauna along elevation gradients in Himalayan cold deserts

High-elevation cold deserts in Tibet and Himalaya are one of the most extreme environments. One consequence is that the diversity of macrofauna in this environment is often limited, and soil microorganisms have a more influential role in governing key surface and subsurface bioprocesses. High-elevation soil microfauna represent important components of cold ecosystems and dominant consumers of microbial communities. Still little is known about their diversity and distribution on the edge of their reproductive and metabolic abilities. In this study, we disentangle the impact of elevation and soil chemistry on diversity and distribution of rotifers, nematodes and tardigrades and their most frequent feeding strategies (microbial filter-feeders, bacterivores, fungivores, root-fungal feeders, omnivores) along two contrasting altitudinal gradients in Indian NW Himalaya (Zanskar transect from 3805 to 4714 m a.s.l.) and southwestern Tibet (Tso Moriri transect from 4477 to 6176 m a.s.l.), using a combination of multivariate analysis, variation partitioning and generalized additive models. Zanskar transect had higher precipitation, soil moisture, organic matter and available nutrients than dry Tso Moriri transect. In total, 40 species of nematodes, 19 rotifers and 1 tardigrade were discovered. Species richness and total abundance of rotifers and nematodes showed mid-elevation peaks in both investigated transects. The optimum for rotifers was found at higher elevation than for nematodes. Diversity and distribution of soil microfauna was best explained by soil nitrogen, phosphorus and organic matter. More fertile soils hosted more diverse and abundant faunal communities. In Tso Moriri, bacterivores represented 60% of all nematodes, fungivores 35%, root-fungal feeders 1% and omnivores 3%. For Zanskar the respective proportions were 21%, 13%, 56% and 9%. Elevational optima of different feeding strategies occurred in Zanskar in one elevation zone (4400–4500 m), while in Tso Moriri each feeding strategy had their unique optima with fungivores at 5300 m (steppes), bacterivores at 5500 m (alpine grassland), filter-feeders at 5600 m and predators and omnivores above 5700 m (subnival zone). Our results shed light on the diversity of microfauna in the high-elevation cold deserts and disentangle the role of different ecological filters in structuring microfaunal communities in the rapidly-warming Himalayas.

Environmental hazard assessment of contaminated soils in Antarctica: Using a structured tier 1 approach to inform decision-making

Generally, Antarctica is considered to be an untouched area of the planet; however, the region's ecosystems have been subject to increased human pressure for at least the past half-century. This study assessed soils of Fildes Peninsula, where trace element pollution is thought to prevail. Four soil samples were collected from different locations and assessed following tier 1 methodologies for chemical and ecotoxicological lines of evidence (LoE) used in typical soil Environmental Risk Assessment (ERA). Trace element quantification was run on soil samples and sequential extracts, and elutriates were used to address their ecotoxicity using a standard ecotoxicological battery. The highest levels of trace elements were found for Cr, Cu, Ni and Zn, which were well above baseline levels in two sites located near previously identified contamination sources. Trace element concentrations in soils were compared with soil quality guidelines to estimate the contribution of the chemical LoE for integrated risk calculations; risk was found high, above 0.5 for all samples. Total concentrations in soil were consistent with corresponding sequentially extracted percentages, with Cu and Zn being the most bioavailable elements. Bacteria did not respond consistently to the elutriate samples and cladocerans did not respond at all. In contrast, the growth of microalgae and macrophytes was significantly impaired by elutriates of all soil samples, consistently to estimated trace element concentrations in the elutriate matrix. These results translated into lower risk values for the ecotoxicological compared to the chemical LoE. Nevertheless, integrated risk calculations generated either an immediate recommendation for further analysis to better understand the hazardous potential of the tested soils or showed that the soils could not adequately sustain natural ecosystem functions. This study suggests that the soil ecosystem in Fildes has been inadequately protected and supports previous claims on the need to reinforce protection measures and remediation activities.

Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica

The potential impact of environmental change on terrestrial Antarctic ecosystems can be explored by inspecting biodiversity patterns across large-scale gradients. Unfortunately, morphology-based surveys of Antarctic invertebrates are time-consuming and limited by the cryptic nature of many taxa. We used biodiversity information derived from high-throughput sequencing (HTS) to elucidate the relationship between soil properties and invertebrate biodiversity in the Prince Charles Mountains, East Antarctica. Across 136 analysed soil samples collected from Mount Menzies, Mawson Escarpment and Lake Terrasovoje, we found invertebrate distribution in the Prince Charles Mountains significantly influenced by soil salinity and/or sulfur content. Phyla Tardigrada and Arachnida occurred predominantly in low-salinity substrates with abundant nutrients, whereas Bdelloidea (Rotifera) and Chromadorea (Nematoda) were more common in highly saline substrates. A significant correlation between invertebrate occurrence, soil salinity and time since deglaciation indicates that terrain age indirectly influences Antarctic terrestrial biodiversity, with more recently deglaciated areas supporting greater diversity. Our study demonstrates the value of HTS metabarcoding to investigate environmental constraints on inconspicuous soil biodiversity across large spatial scales.

Genetic diversity among populations of Antarctic springtails (Collembola) within the Mackay Glacier ecotone

Climate changes are likely to have major influences on the distribution and abundance of Antarctic terrestrial biota. To assess arthropod distribution and diversity within the Ross Sea region, we examined mitochondrial DNA (COI) sequences for three currently recognized species of springtail (Collembola) collected from sites in the vicinity, and to the north of, the Mackay Glacier (77°S). This area acts as a transition between two biogeographic regions (northern and southern Victoria Land). We found populations of highly divergent individuals (5%-11.3% intraspecific sequence divergence) for each of the three putative springtail species, suggesting the possibility of cryptic diversity. Based on molecular clock estimates, these divergent lineages are likely to have been isolated for 3-5 million years. It was during this time that the Western Antarctic Ice Sheet (WAIS) was likely to have completely collapsed, potentially facilitating springtail dispersal via rafting on running waters and open seaways. The reformation of the WAIS would have isolated newly established populations, with subsequent dispersal restricted by glaciers and ice-covered areas. Given the currently limited distributions for these genetically divergent populations, any future changes in species' distributions can be easily tracked through the DNA barcoding of springtails from within the Mackay Glacier ecotone.

Evaluating a multigene environmental DNA approach for biodiversity assessment

Background

There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient.

Results

From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures.

Conclusions

Using a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods.

Electronic supplementary material

The online version of this article (doi:10.1186/s13742-015-0086-1) contains supplementary material, which is available to authorized users.

Mitochondrial DNA analyses reveal widespread tardigrade diversity in Antarctica

Antarctica contains some of the most challenging environmental conditions on the planet due to freezing temperatures, prolonged winters and lack of liquid water. Whereas 99.7% of Antarctica is permanently covered by ice and snow, some coastal areas and mountain ridges have remained ice-free and are able to sustain populations of microinvertebrates. Tardigrades are one of the more dominant groups of microfauna in soil and limno-terrestrial habitats, but little is known of their diversity and distribution across Antarctica. Here, we examine tardigrades sampled from across an extensive region of continental Antarctica, and analyse and compare their partial mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences with those from the Antarctic Peninsula, maritime and sub-Antarctica, Tierra del Fuego and other worldwide locations in order to recognise operational taxonomic units (OTUs). From 439 new tardigrade COI sequences, we identified 98 unique haplotypes (85 from Antarctica) belonging to Acutuncus, Diphascon, Echiniscus, Macrobiotus, Milnesium and unidentified Parachela. Operational taxonomic units were delimited by Poisson tree processes and general mixed Yule coalescent methods, resulting in 58 and 55 putative species, respectively. Most tardigrades appear to be locally endemic (i.e. restricted to a single geographic region), but some (e.g. Acutuncus antarcticus (Richters, 1904)) are widespread across continental Antarctica. Our molecular results reveal: (i) greater diversity than has previously been appreciated with distinct OTUs that potentially represent undescribed species, and (ii) a lack of connectivity between most OTUs from continental Antarctica and those from other Antarctic geographical zones.