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.

Wide divergence of fungal communities inhabiting rocks and soils in a hyper-arid Antarctic desert

Highly simplified microbial communities colonise rocks and soils of continental Antarctica ice-free deserts. These two habitats impose different selection pressures on organisms, yet the possible filtering effects on the diversity and composition of microbial communities have not hitherto been fully characterised. We hence compared fungal communities in rocks and soils in three localities of inner Victoria Land. We found low fungal diversity in both substrates, with a mean species richness of 28 across all samples, and significantly lower diversity in rocks than in soils. Rock and soil communities were strongly differentiated, with a multinomial species classification method identifying just three out of 328 taxa as generalists with no affinity for either substrate. Rocks were characterised by a higher abundance of lichen-forming fungi (typically Buellia, Carbonea, Pleopsidium, Lecanora, and Lecidea), possibly owing to the more protected environment and the porosity of rocks permitting photosynthetic activity. In contrast, soils were dominated by obligate yeasts (typically Naganishia and Meyerozyma), the abundances of which were correlated with edaphic factors, and the black yeast Cryomyces. Our study suggests that strong differences in selection pressures may account for the wide divergences of fungal communities in rocks and soils of inner Victoria Land.

Connecting the multiple dimensions of global soil fungal diversity

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Rapid Response to Experimental Warming of a Microbial Community Inhabiting High Arctic Patterned Ground Soil

The influence of climate change on microbial communities inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic is poorly understood. Here, in a four-year experiment on Svalbard, we warmed patterned ground soil with open top chambers and biannually irrigated the soil to predict the responses of its microbial community to rising temperatures and precipitation. A 1 °C rise in summertime soil temperature caused 44% and 78% increases in CO₂ efflux and CH₄ consumption, respectively, and a 32% increase in the frequency of bacterial 16S ribosomal RNA genes. Bacterial alpha diversity was unaffected by the treatments, but, of the 40 most frequent bacterial taxa, warming caused 44-45% reductions in the relative abundances of a Sphingomonas sp. and Ferruginibacter sp. and 33-91% increases in those of a Phenylobacterium sp. and a member of the Acetobacteraceae. Warming did not influence the frequency of fungal internal transcribed spacer 2 copies, and irrigation had no effects on the measured variables. Our study suggests rapid changes to the activities and abundances of microbes, and particularly bacteria, in High Arctic patterned ground soils as they warm. At current rates of soil warming on Svalbard (0.8 °C per decade), we anticipate that similar effects to those reported here will manifest themselves in the natural environment by approximately the mid 2030s.

Experimental warming increases fungal alpha diversity in an oligotrophic maritime Antarctic soil

The climate of maritime Antarctica has altered since the 1950s. However, the effects of increased temperature, precipitation and organic carbon and nitrogen availability on the fungal communities inhabiting the barren and oligotrophic fellfield soils that are widespread across the region are poorly understood. Here, we test how warming with open top chambers (OTCs), irrigation and the organic substrates glucose, glycine and tryptone soy broth (TSB) influence a fungal community inhabiting an oligotrophic maritime Antarctic fellfield soil. In contrast with studies in vegetated soils at lower latitudes, OTCs increased fungal community alpha diversity (Simpson's index and evenness) by 102-142% in unamended soil after 5 years. Conversely, OTCs had few effects on diversity in substrate-amended soils, with their only main effects, in glycine-amended soils, being attributable to an abundance of Pseudogymnoascus. The substrates reduced alpha and beta diversity metrics by 18-63%, altered community composition and elevated soil fungal DNA concentrations by 1-2 orders of magnitude after 5 years. In glycine-amended soil, OTCs decreased DNA concentrations by 57% and increased the relative abundance of the yeast Vishniacozyma by 45-fold. The relative abundance of the yeast Gelidatrema declined by 78% in chambered soil and increased by 1.9-fold in irrigated soil. Fungal DNA concentrations were also halved by irrigation in TSB-amended soils. In support of regional- and continental-scale studies across climatic gradients, the observations indicate that soil fungal alpha diversity in maritime Antarctica will increase as the region warms, but suggest that the accumulation of organic carbon and nitrogen compounds in fellfield soils arising from expanding plant populations are likely, in time, to attenuate the positive effects of warming on diversity.

Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

The growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes.

Fine hyphal coils in the liverwort Cephaloziella varians increase in frequency in response to experimental warming in maritime Antarctica

Previous studies have shown changes to the frequencies of hyphal coils and other fungal structures in leafy liverwort tissues across latitudinal transects through Antarctica. Although suggestive of a role of temperature in determining the frequencies of fungal structures, these studies could not exclude the possibility that other factors which alter at lower latitudes-notably liquid water availability-were responsible for the observed patterns of fungal colonisation. Here, in a field experiment in maritime Antarctica, the effects of warming with open top chambers (OTCs) on the frequencies of fungal structures in the leafy liverwort Cephaloziella varians were determined. At five samplings of the experiment taking place 5-10 years after its deployment, OTCs, which increased the summertime temperature of C. varians mats by 1.1 °C, but had no measurable effects on mat moisture concentration, were found to double the frequencies of fine hyphal coils in liverwort tissues. Over the duration of the experiment, the OTCs also significantly increased the frequency of rhizoids on C. varians stems, but had no effects on the frequencies of coarse hyphal coils, dark septate hyphae, hyaline septate hyphae, or hyphal colonisation of rhizoids. Given that C. varians can be recovered from frozen peatbank cores, it is proposed that the abundance of fine hyphal coils in its tissues might be used as a signal of recent climate warming on the Antarctic Peninsula.

Regional Diversity of Maritime Antarctic Soil Fungi and Predicted Responses of Guilds and Growth Forms to Climate Change

We report a metabarcoding study documenting the fungal taxa in 29 barren fellfield soils sampled from along a 1,650 km transect encompassing almost the entire maritime Antarctic (60-72°S) and the environmental factors structuring the richness, relative abundance, and taxonomic composition of three guilds and growth forms. The richness of the lichenised fungal guild, which accounted for 19% of the total fungal community, was positively associated with mean annual surface air temperature (MASAT), with an increase of 1.7 operational taxonomic units (OTUs) of lichenised fungi per degree Celsius rise in air temperature. Soil Mn concentration, MASAT, C:N ratio, and pH value determined the taxonomic composition of the lichenised guild, and the relative abundance of the guild was best predicted by soil Mn concentration. There was a 3% decrease in the relative abundance of the saprotrophic fungal guild in the total community for each degree Celsius rise in air temperature, and the OTU richness of the guild, which accounted for 39% of the community, was negatively associated with Mn concentration. The taxonomic composition of the saprotrophic guild varied with MASAT, pH value, and Mn, NH4 +-N, and SO4 2- concentrations. The richness of the yeast community, which comprised 3% of the total fungal community, was positively associated with soil K concentration, with its composition being determined by C:N ratio. In contrast with a similar study in the Arctic, the relative abundance and richness of lichenised fungi declined between 60°S and 69°S, with those of saprotrophic Agaricales also declining sharply in soils beyond 63°S. Basidiomycota, which accounted for 4% of reads, were much less frequent than in vegetated soils at lower latitudes, with the Ascomycota (70% of reads) being the dominant phylum. We conclude that the richness, relative abundance, and taxonomic composition of guilds and growth forms of maritime Antarctic soil fungi are influenced by air temperature and edaphic factors, with implications for the soils of the region as its climate changes during the 21st century.

A Previously Undescribed Helotialean Fungus That Is Superabundant in Soil Under Maritime Antarctic Higher Plants

We report a previously undescribed member of the Helotiales that is superabundant in soils at two maritime Antarctic islands under Antarctic Hairgrass (Deschampsia antarctica Desv.). High throughput sequencing showed that up to 92% of DNA reads, and 68% of RNA reads, in soils from the islands were accounted for by the fungus. Sequencing of the large subunit region of ribosomal (r)DNA places the fungus close to the Pezizellaceae, Porodiplodiaceae, and Sclerotiniaceae, with analyses of internal transcribed spacer regions of rDNA indicating that it has affinities to previously unnamed soil and root fungi from alpine, cool temperate and Low Arctic regions. The fungus was found to be most frequent in soils containing C aged to 1,000-1,200 years before present. The relative abundances of its DNA and RNA reads were positively associated with soil carbon and nitrogen concentrations and δ13C values, with the relative abundance of its DNA being negatively associated with soil pH value. An isolate of the fungus produces flask-shaped phialides with a pronounced venter bearing masses of conidia measuring 4.5-6(7) × 1.8-2.5 μm, suggestive of anamorphic Chalara. Enzymatic studies indicate that the isolate strongly synthesizes the extracellular enzyme acid phosphatase, and also exhibits alkaline phosphatase and naphthol-AS-BI-phosphohydrolase activities. Ecophysiological measurements indicate optimal hyphal growth of the isolate at a pH of 4.2-4.5 and a water potential of -0.66 MPa. The isolate is a psychrotroph, exhibiting measureable hyphal growth at -2°C, optimal hyphal extension rate at 15°C and negligible growth at 25°C. It is proposed that the rising temperatures that are predicted to occur in maritime Antarctica later this century will increase the growth rate of the fungus, with the potential loss of ancient C from soils. Analyses using the GlobalFungi Database indicate that the fungus is present in cold, acidic soils on all continents. We advocate further studies to identify whether it is superabundant in soils under D. antarctica elsewhere in maritime Antarctica, and for further isolates to be obtained so that the species can be formally described.

Inhibitory effects of climate change on the growth and extracellular enzyme activities of a widespread Antarctic soil fungus

Temperatures approaching or exceeding 20°C have been measured during summer in polar regions at the surfaces of barren fellfield soils under cloudless skies around solar noon. However, despite the upper temperature limit for the growth of cold-adapted microbes-which are abundant in polar soils and have pivotal roles in nutrient cycling-typically being close to this temperature, previous studies have not addressed the consequences of climate change for the metabolism of these organisms in the natural environment. Here in a 5-year field experiment on Alexander Island in the southern maritime Antarctic, we show that the abundance of Pseudogymnoascus roseus, the most widespread decomposer fungus in maritime Antarctic fellfield soils, is reduced by 1-2 orders of magnitude when irrigated and nutrient-amended soils are warmed to >20°C during summer. Laboratory experiments under conditions mimicking those during midsummer in the natural environment indicated that the hyphal extension rates of P. roseus isolates and the activities of five extracellular enzymes are reduced by 54%-96% at high water availability after exposure to temperatures cycling daily from 2 to 21°C and 2 to 24°C, relative to temperatures cycling from 2 to 18°C. Given that the temperatures of surface soils at the study site already reach 19°C during midsummer, the observations reported here suggest that, at predicted rates of warming arising from moderate greenhouse gas emissions, inhibitory effects of climate change on the metabolism of P. roseus could manifest themselves within the next few decades. Furthermore, with peak temperatures at the surfaces of fellfield soils at other maritime Antarctic locations and in High Arctic and alpine regions already exceeding 20°C during summer, the observations suggest that climate warming has the potential to inhibit the growth of other cold-adapted microbes, with negative effects on soils as the Earth's climate continues to warm.

Functional roles of microbial symbionts in plant cold tolerance

In this review, we examine the functional roles of microbial symbionts in plant tolerance to cold and freezing stresses. The impacts of symbionts on antioxidant activity, hormonal signaling and host osmotic balance are described, including the effects of the bacterial endosymbionts Burkholderia, Pseudomonas and Azospirillum on photosynthesis and the accumulation of carbohydrates such as trehalose and raffinose that improve cell osmotic regulation and plasma membrane integrity. The influence of root fungal endophytes and arbuscular mycorrhizal fungi on plant physiology at low temperatures, for example their effects on nutrient acquisition and the accumulation of indole-3-acetic acid and antioxidants in tissues, are also reviewed. Meta-analyses are presented showing that aspects of plant performance (shoot biomass, relative water content, sugar and proline concentrations and F_v /F_m ) are enhanced in symbiotic plants at low (-1 to 15 °C), but not at high (20-26 °C), temperatures. We discuss the implications of microbial symbionts for plant performance at low and sub-zero temperatures in the natural environment and propose future directions for research into the effects of symbionts on the cold and freezing tolerances of plants, concluding that further studies should routinely incorporate symbiotic microbes in their experimental designs.

Bacterial Community Composition and Diversity Respond to Nutrient Amendment but Not Warming in a Maritime Antarctic Soil

A resumption of climate warming in maritime Antarctica, arising from continued greenhouse gas emissions to the atmosphere, is predicted to lead to further expansions of plant populations across the region, with consequent increases in nutrient inputs to soils. Here, we test the main and interactive effects of warming, applied with open top chambers (OTCs), and nutrient amendment with tryptic soy broth (TSB), an artificial growth substrate, on bacterial community composition and diversity using Illumina sequencing of 16S rRNA genes in soil from a field experiment in the southern maritime Antarctic. Substantial effects of TSB application on bacterial communities were identified after 49 months, including reduced diversity, altered phylogenetic community assembly processes, increased Proteobacteria-to-Acidobacteria ratios and significant divergence in community composition, notably increases in the relative abundances of the gram-positive genera Arthrobacter, Paeniglutamicibacter and Planococcus. Contrary to previous observations from other maritime Antarctic field warming experiments, we recorded no effects of warming with OTCs, or interactive effects of OTCs and TSB application, on bacterial community composition or diversity. Based on these findings, we conclude that further warming of the maritime Antarctic is unlikely to influence soil bacterial community composition or diversity directly, but that increased nutrient inputs arising from enhanced plant growth across the region may affect the composition of soil bacterial communities, with possible effects on ecosystem productivity.

Angiosperm symbioses with non-mycorrhizal fungal partners enhance N acquisition from ancient organic matter in a warming maritime Antarctic

In contrast to the situation in plants inhabiting most of the world’s ecosystems, mycorrhizal fungi are usually absent from roots of the only two native vascular plant species of maritime Antarctica, Deschampsia antarctica and Colobanthus quitensis. Instead, a range of ascomycete fungi, termed dark septate endophytes (DSEs), frequently colonise the roots of these plant species. We demonstrate that colonisation of Antarctic vascular plants by DSEs facilitates not only the acquisition of organic nitrogen as early protein breakdown products, but also as non‐proteinaceous d‐amino acids and their short peptides, accumulated in slowly‐decomposing organic matter, such as moss peat. Our findings suggest that, in a warming maritime Antarctic, this symbiosis has a key role in accelerating the replacement of formerly dominant moss communities by vascular plants, and in increasing the rate at which ancient carbon stores laid down as moss peat over centuries or millennia are returned to the atmosphere as CO₂.

Microbial community drivers of PK/NRP gene diversity in selected global soils

BACKGROUND

The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils.

RESULTS

Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP.

CONCLUSIONS

The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites.

Endemic and cosmopolitan fungal taxa exhibit differential abundances in total and active communities of Antarctic soils

Our understanding of the diversity and community dynamics of soil fungi has increased greatly through the use of DNA-based identification. Community characterization of metabolically active communities via RNA sequencing has previously revealed differences between 'active' and 'total' fungal communities, which may be influenced by the persistence of DNA from nonactive components. However, it is not known how fungal traits influence their prevalence in these contrasting community profiles. In this study, we coextracted DNA and RNA from soil collected from three Antarctic islands to test for differences between total and active soil fungal communities. By matching these geographically isolated fungi against a global dataset of soil fungi, we show that widely dispersed taxa are often more abundant in the total community, whilst taxa restricted to Antarctica are more likely to have higher abundance in the active community. In addition, we find that active communities have lower richness, and show a reduction in the abundance of the most dominant fungi, whilst there are consistent differences in the abundances of certain taxonomic groups between the total and active communities. These results suggest that the views of soil fungal communities offered by DNA- and RNA-based characterization differ in predictable ways.

Snow algae communities in Antarctica: metabolic and taxonomic composition

Snow algae are found in snowfields across cold regions of the planet, forming highly visible red and green patches below and on the snow surface. In Antarctica, they contribute significantly to terrestrial net primary productivity due to the paucity of land plants, but our knowledge of these communities is limited. Here we provide the first description of the metabolic and species diversity of green and red snow algae communities from four locations in Ryder Bay (Adelaide Island, 68°S), Antarctic Peninsula. During the 2015 austral summer season, we collected samples to measure the metabolic composition of snow algae communities and determined the species composition of these communities using metabarcoding. Green communities were protein-rich, had a high chlorophyll content and contained many metabolites associated with nitrogen and amino acid metabolism. Red communities had a higher carotenoid content and contained more metabolites associated with carbohydrate and fatty acid metabolism. Chloromonas, Chlamydomonas and Chlorella were found in green blooms but only Chloromonas was detected in red blooms. Both communities also contained bacteria, protists and fungi. These data show the complexity and variation within snow algae communities in Antarctica and provide initial insights into the contribution they make to ecosystem functioning.

Arbuscular mycorrhizas are present on Spitsbergen

A previous study of 76 plant species on Spitsbergen in the High Arctic concluded that structures resembling arbuscular mycorrhizas were absent from roots. Here, we report a survey examining the roots of 13 grass and forb species collected from 12 sites on the island for arbuscular mycorrhizal (AM) colonisation. Of the 102 individuals collected, we recorded AM endophytes in the roots of 41 plants of 11 species (Alopecurus ovatus, Deschampsia alpina, Festuca rubra ssp. richardsonii, putative viviparous hybrids of Poa arctica and Poa pratensis, Poa arctica ssp. arctica, Trisetum spicatum, Coptidium spitsbergense, Ranunculus nivalis, Ranunculus pygmaeus, Ranunculus sulphureus and Taraxacum arcticum) sampled from 10 sites. Both coarse AM endophyte, with hyphae of 5-10 μm width, vesicles and occasional arbuscules, and fine endophyte, consisting of hyphae of 1-3 μm width and sparse arbuscules, were recorded in roots. Coarse AM hyphae, vesicles, arbuscules and fine endophyte hyphae occupied 1.0-30.7, 0.8-18.3, 0.7-11.9 and 0.7-12.8% of the root lengths of colonised plants, respectively. Principal component analysis indicated no associations between the abundances of AM structures in roots and edaphic factors. We conclude that the AM symbiosis is present in grass and forb roots on Spitsbergen.

Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils

The ever increasing microbial resistome means there is an urgent need for new antibiotics. Metagenomics is an underexploited tool in the field of drug discovery. In this study we aimed to produce a new updated assay for the discovery of biosynthetic gene clusters encoding bioactive secondary metabolites. PCR assays targeting the polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) were developed. A range of European soils were tested for their biosynthetic potential using clone libraries developed from metagenomic DNA. Results revealed a surprising number of NRPS and PKS clones with similarity to rare Actinomycetes. Many of the clones tested were phylogenetically divergent suggesting they were fragments from novel NRPS and PKS gene clusters. Soils did not appear to cluster by location but did represent NRPS and PKS clones of diverse taxonomic origin. Fosmid libraries were constructed from Cuban and Antarctic soil samples; 17 fosmids were positive for NRPS domains suggesting a hit rate of less than 1 in 10 genomes. NRPS hits had low similarities to both rare Actinobacteria and Proteobacteria; they also clustered with known antibiotic producers suggesting they may encode for pathways producing novel bioactive compounds. In conclusion we designed an assay capable of detecting divergent NRPS and PKS gene clusters from the rare biosphere; when tested on soil samples results suggest the majority of NRPS and PKS pathways and hence bioactive metabolites are yet to be discovered.

Metagenomic analysis of a southern maritime antarctic soil

Our current understanding of Antarctic soils is derived from direct culture on selective media, biodiversity studies based on clone library construction and analysis, quantitative PCR amplification of specific gene sequences and the application of generic microarrays for microbial community analysis. Here, we investigated the biodiversity and functional potential of a soil community at Mars Oasis on Alexander Island in the southern Maritime Antarctic, by applying 454 pyrosequencing technology to a metagenomic library constructed from soil genomic DNA. The results suggest that the commonly cited range of phylotypes used in clone library construction and analysis of 78–730 OTUs (de-replicated to 30–140) provides low coverage of the major groups present (∼5%). The vast majority of functional genes (>77%) were for structure, carbohydrate metabolism, and DNA/RNA processing and modification. This study suggests that prokaryotic diversity in Antarctic terrestrial environments appears to be limited at the generic level, with Proteobacteria, Actinobacteria being common. Cyanobacteria were surprisingly under-represented at 3.4% of sequences, although ∼1% of the genes identified were involved in CO₂ fixation. At the sequence level there appeared to be much greater heterogeneity, and this might be due to high divergence within the relatively restricted lineages which have successfully colonized Antarctic terrestrial environments.

A meta-analysis of plant responses to dark septate root endophytes

• Dark septate endophytes (DSE) frequently colonize roots in the natural environment, but the effects of these fungi on plants are obscure, with previous studies indicating negative, neutral or positive effects on plant performance. • In order to reach a consensus for how DSE influence plant performance, meta-analyses were performed on data from 18 research articles, in which plants had been inoculated with DSE in sterile substrates. • Negative effects of DSE on plant performance were not recorded. Positive effects were identified on total, shoot and root biomass, and on shoot nitrogen (N) and phosphorus contents, with increases of 26-103% in these parameters for plants inoculated with DSE, relative to uninoculated controls. Inoculation increased total, shoot and root biomass by 52-138% when plants had not been supplied with additional inorganic N, or when all, or the majority, of N was supplied in organic form. Inoculation with the DSE Phialocephala fortinii was found to increase shoot and root biomass, shoot P concentration and shoot N content by 44-116%, relative to uninoculated controls. • The analyses here suggest that DSE enhance plant performance under controlled conditions, particularly when all, or the majority, of N is available in organic form.

Structural changes to a mycothallus along a latitudinal transect through the maritime and sub-Antarctic

Previous studies have shown the leafy liverwort Cephaloziella varians to associate consistently with fungi, typically the ericoid mycorrhizal symbiont Rhizoscyphus ericae, across a wide latitudinal gradient in the maritime and sub-Antarctic. Hitherto, however, there are no quantitative data on the intensity of colonisation of C. varians by fungal structures in the natural environment and how colonisation might vary with changing environmental conditions. A study is hence reported showing that the frequency of colonisation by fungal structures of C. varians alters along a latitudinal transect from South Georgia (54° S, 38° W) to Moutonnée Valley on Alexander Island (71° S, 68° W). The percentage of stem length colonised by dark septate (DS) hyphae increased significantly along the transect, from 30% at South Georgia to 97% at Moutonnée Valley. In contrast, the percentage of stem length colonised by hyaline hyphae decreased significantly, from 85% at South Georgia to 13% at Moutonnée Valley, and that colonised by hyphal coils similarly decreased from 71% at the former location to 15% at the latter. The frequencies of DS hyphae were negatively associated with mean annual and seasonal air temperatures, whereas those of hyaline septate hyphae and hyphal coils were positively associated with air temperatures. Coils at northerly locations were more convoluted than those at southerly locations. The data indicate that hyphal coils, usually associated with nutrient exchange between partners in ericoid mycorrhizas, do form in C. varians tissues in the maritime and sub-Antarctic, but that the frequency of these structures diminishes in colder habitats.

Sebacinales are associates of the leafy liverwort Lophozia excisa in the southern maritime Antarctic

The leafy liverwort Lophozia excisa, which is colonised by basidiomycete fungi in other biomes and which evidence suggests may be colonised by mycorrhizal fungi in Antarctica, was sampled from Léonie Island in the southern maritime Antarctic (67 degrees 36' S, 68 degrees 21' W). Microscopic examination of plants indicated that fungal hyphae colonised 78% of the rhizoids of the liverwort, apparently by entering the tips of rhizoids prior to growing into their bases, where they formed hyphal coils. Extensive colonisation of stem medullary cells by hyphae was also observed. DNA was extracted from surface-sterilised liverwort tissues and sequenced following nested PCR, using the primer set ITS1F/TW14, followed by a second round of amplification using the ITSSeb3/TW13 primer set. Neighbour-joining analyses showed that the sequences obtained nested in Sebacinales clade B as a 100% supported sister group to Sebacinales sequences from the leafy liverworts Lophozia sudetica, L. incisa and Calypogeia muelleriana sampled from Europe. Direct PCR using the fungal specific primer set ITS1F/ITS4 similarly identified fungi belonging to Sebacinales clade B as the principal colonists of L. excisa tissues. These observations indicate the presence of a second mycothallus in Antarctica and support the previous suggestion that the Sebacinales has a wide geographical distribution.

Minimal influence of water and nutrient content on the bacterial community composition of a maritime Antarctic soil

Bacterial community composition was determined by culture-independent PCR-based methods in two soils differing markedly in their water, C, N and P contents sampled from Mars Oasis on Alexander Island, western Antarctic Peninsula. 16S rRNA sequences of the phyla Actinobacteria, Cyanobacteria, α-Proteobacteria and Acidobacteria were commonly (> 8% frequency) obtained from soil. Those of β-, γ- and δ-Proteobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, Planctomycetes, Gemmatimonadetes and Firmicutes were less frequent. Comparisons of slopes of collector's curves and the Shannon-Weiner diversity index indicated no difference in overall bacterial diversity between the two soils, although sequences of δ-Proteobacteria and the cyanobacterial genus Leptolyngbya were more commonly derived from the soil with the higher water and nutrient content. The data suggest that different levels of soil water, C, N and P have only a minor effect on the bacterial community composition of maritime Antarctic soils.

Nitrogen form influences the response of Deschampsia antarctica to dark septate root endophytes

Fungi with dematiaceous septate hyphae, termed dark septate endophytes (DSE), are common in plant roots, particularly in cold-stressed habitats, but their effects on their host plants remain obscure. Here, we report a study that assessed the effects of six DSE on the growth and nutrient balance of Deschampsia antarctica when plants were supplied with the same amount of nitrogen in organic (casein hydrolysate) or inorganic (ammonium sulphate) form under controlled conditions. After 60 days, the DSE, that had each been isolated from D. antarctica and which analyses of internal transcribed spacer and large subunit regions indicated were similar to members of the Helotiales (Oculimacula yallundae, Mollisia and Tapesia spp.) and unassigned anamorphic ascomycetes, typically had no effect on, or reduced by 33-71%, shoot and root dry weights relative to uninoculated controls when plants had been supplied with nitrogen in inorganic form. In contrast, the DSE usually enhanced shoot and root dry weights by 51-247% when plants had been supplied with organic nitrogen. In the presence of inorganic nitrogen, only sporadic effects of DSE were recorded on shoot and root nitrogen or phosphorus concentrations, whereas in the presence of organic nitrogen, three to six of the DSE isolates increased shoot and root nitrogen and phosphorus contents. Most of the isolates decreased the phosphorus concentrations of shoots and roots when plants had been supplied with nitrogen in organic form. Our data suggest that DSE are able to mineralise peptides and amino acids in the rhizosphere, making nitrogen more freely available to roots.

Patterns of bacterial diversity across a range of Antarctic terrestrial habitats

Although soil-borne bacteria represent the world's greatest source of biological diversity, it is not well understood whether extreme environmental conditions, such as those found in Antarctic habitats, result in reduced soil-borne microbial diversity. To address this issue, patterns of bacterial diversity were studied in soils sampled along a > 3200 km southern polar transect spanning a gradient of increased climate severity over 27 degrees of latitude. Vegetated and fell-field plots were sampled at the Falkland (51 degrees S), South Georgia (54 degrees S), Signy (60 degrees S) and Anchorage Islands (67 degrees S), while bare frost-sorted soil polygons were examined at Fossil Bluff (71 degrees S), Mars Oasis (72 degrees S), Coal Nunatak (72 degrees S) and the Ellsworth Mountains (78 degrees S). Bacterial 16S rRNA gene sequences were recovered subsequent to direct DNA extraction from soil, polymerase chain reaction amplification and cloning. Although bacterial diversity was observed to decline with increased latitude, habitat-specific patterns appeared to also be important. Namely, a negative relationship was found between bacterial diversity and latitude for fell-field soils, but no such pattern was observed for vegetated sites. The Mars Oasis site, previously identified as a biodiversity hotspot within this region, proved exceptional within the study transect, with unusually high bacterial diversity. In independent analyses, geographical distance and vegetation cover were found to significantly influence bacterial community composition. These results provide insight into the factors shaping the composition of bacterial communities in Antarctic terrestrial habitats and support the notion that bacterial diversity declines with increased climatic severity.

Widespread association between the ericoid mycorrhizal fungus Rhizoscyphus ericae and a leafy liverwort in the maritime and sub-Antarctic

A recent study identified a fungal isolate from the Antarctic leafy liverwort Cephaloziella varians as the ericoid mycorrhizal associate Rhizoscyphus ericae. However, nothing is known about the wider Antarctic distribution of R. ericae in C. varians, and inoculation experiments confirming the ability of the fungus to form coils in the liverwort are lacking. Using direct isolation and baiting with Vaccinium macrocarpon seedlings, fungi were isolated from C. varians sampled from eight sites across a 1875-km transect through sub- and maritime Antarctica. The ability of an isolate to form coils in aseptically grown C. varians was also tested. Fungi with 98-99% sequence identity to R. ericae internal transcribed spacer (ITS) region and partial large subunit ribosomal (r)DNA sequences were frequently isolated from C. varians at all sites sampled. The EF4/Fung5 primer set did not amplify small subunit rDNA from three of five R. ericae isolates, probably accounting for the reported absence of the fungus from C. varians in a previous study. Rhizoscyphus ericae was found to colonize aseptically-grown C. varians intracellularly, forming hyphal coils. This study shows that the association between R. ericae and C. varians is apparently widespread in Antarctica, and confirms that R. ericae is at least in part responsible for the formation of the coils observed in rhizoids of field-collected C. varians.

Survival of antarctic soil metazoans at -80 degree C for six years

A sample of the liverwort Cephaloziella varians was collected on 1 January 1999 at Rothera Point on the Wright Peninsula, Adelaide Island, western Antarctic Peninsula and was partially dried and then frozen at -80 degree C. The sample was rapidly defrosted to c. 10 degree C after six years and two months of storage at this temperature. Nematodes, tardigrades and a bdelloid rotifer present in the sample were found to have survived. Of the 159 nematodes recovered from the sample, 49 (31%) were alive: of the tardigrades and rotifers, two of 15 (13%) and one of 48 (2%) had survived, respectively. A Chi-square test showed that there was a significant association between nematode taxon and survival: a greater proportion of Coomansus gerlachei individuals were alive than of Rhyssocolpus paradoxus. A Chi-square test also showed that there was a significant association between phylum and survival: a significantly greater proportion of nematodes or tardigrades were alive than of bdelloid rotifers. We conclude that Antarctic soil metazoans are capable of surviving long-term exposure to low sub-zero temperatures and that there may be taxon-specific effects of freezing on survival.

Significant changes in the bacterioplankton community structure of a maritime Antarctic freshwater lake following nutrient enrichment

Nutrient enrichment is known to increase bacterioplankton population density in a variety of Antarctic freshwater lakes. However, relatively little is known about the associated changes in species composition. In this study, the bacterioplankton community composition of one such lake was studied following natural nutrient enrichment to investigate the resistance of the system to environmental change. Heywood Lake is an enriched freshwater maritime Antarctic lake, with nitrogen and phosphorus concentrations significantly higher than its more oligotrophic neighbours (by at least an order of magnitude). This major change in lake chemistry has occurred following large increases in the fur seal population over the last 30 years. Using analysis of 16S rRNA gene fragments, fatty acid methyl ester analysis, denaturing gradient gel electrophoresis and fluorescence in situ hybridization, significant changes are reported in lake microbiology which have resulted in a distinct bacterioplankton community. In comparison to its more oligotrophic neighbours, nutrient-enriched Heywood Lake has a high bacterioplankton population density, reduced species richness and an increasing evenness among key groups. Only 42.3 % of the clones found with > or =97 % similarity to a named genus were also present in adjacent oligotrophic lakes, including three of the dominant groups. Critically, there was an apparent shift in dominance with trophic status (from the beta-Proteobacteria to the Actinobacteria). Other key observations included the absence of a dominant group of Cyanobacteria and the presence of marine bacteria. The significant impact of natural nutrient enrichment on the microbiology of Heywood Lake, therefore, suggests that low-temperature oligotrophic freshwater lake systems might have low resistance to environmental change.

UV-B radiation arising from stratospheric ozone depletion influences the pigmentation of the Antarctic moss Andreaea regularis

Changes to the radiative environment arising from stratospheric ozone (O(3)) depletion and subsequent associations between these changes and the pigmentation of the moss Andreaea regularis were measured in late austral spring and early summer 1998 at Rothera Point on the western Antarctic Peninsula (67 degrees S, 68 degrees W). A strong relationship between O(3) column depth and the ratio of UV-B to PAR irradiance ( F(uv-b)/ F(par)) was recorded at ground level ( r(2)=92%, P<0.001). Weaker, but significant, associations between O(3) column depth and ground level unweighted and biologically effective UV-B radiation (UV-B(be)) were also found. Regression analyses indicated that F(uv-b)/ F(par) was the best predictor for concentrations of UV-B screening pigments and total carotenoids extracted from plant tissues. Concentrations of these pigments were loosely ( r(2)= ca. 30%) but significantly ( P<0.01) positively associated with F(uv-b)/ F(par). Concentrations of UV-B screening pigments were also positively associated with irradiances and daily doses of unweighted UV-B and UV-B(be) radiation. The concentrations of chlorophylls a and b were apparently unaffected by O(3) depletion. The data derived from this study suggest that changes to the radiative environment associated with stratospheric O(3) depletion influence the pigmentation of A. regularis. As a corollary, flavonoids are shown to be present in tissues of A. regularis.

Filamentous ascomycetes inhabiting the rhizoid environment of the liverwort Cephaloziella varians in Antarctica are assessed by direct PCR and cloning

We molecularly assesed the ascomycetous fungal communities inhabiting the rhizoid environment of Cephaloziella varians, collected at Rothera Point on the western Antarctic Peninsula. The RFLP-phenotyped and cloned PCR products of a partial small subunit of the ribosomal RNA gene were sequenced and analyzed with neighbor joining (NJ) and maximum parsimony (MP). Both analyses identified four bootstrap-supported groups: (i) a sister group to Onygenales, (ii) a well-supported clade with Phialocephala fortinii, (iii) a large group of clones nested within Chaetothyriales, and (iv) a group nested within Eurotiales with a likely affinity to the genus Aspergillus. An additional marginally supported clade, including helotialean Hymenoscyphus fructigenus, was detected in the NJ analysis. Placement of one clone (possibly helotialean) was not supported by either analysis. We included Hymenoscyphus ericae (Helotiales) in our analyses to test for its presence in clone libraries. None of our clones showed strongly supported affinity to H. ericae. The culture-independent technique proved useful for assessing the composition of rhizoid fungal communities, although it remains unknown whether any of these fungi colonize C. varians tissues. Direct-community assays of this kind might be best combined with traditional isolation techniques to get a more holistic view of fungi occupying plant tissues.

Solar UV-B radiation inhibits the growth of Antarctic terrestrial fungi

We tested the effects of solar radiation, and UV-B in particular, on the growth of Antarctic terrestrial fungi. The growth responses to solar radiation of five fungi, Geomyces pannorum, Phoma herbarum, Pythium sp., Verticillium sp., and Mortierella parvispora, each isolated from Antarctic terrestrial habitats, were examined on an agar medium in the natural Antarctic environment. A 3-h exposure to solar radiation of >287 nm reduced the hyphal extension rates of all species relative to controls kept in the dark. Pythium sp. cultures exposed to solar radiation for 1.5 h on five consecutive days were most sensitive to radiation of >287 nm, but radiation of >313 nm also inhibited growth to a lesser extent. Radiation of >400 nm had no effect on hyphal growth relative to controls kept in the dark. Short-wave solar UV-B radiation of between 287 and 305 nm inhibited the growth of Pythium sp. hyphae on and below the surface of the agar medium after 24 h, but radiation of > or =345 nm only reduced the growth of surface hyphae. Similar detrimental effects of UV-B on surface and, to a lesser extent, submerged hyphae of all five fungi were shown in the laboratory by using artificial UV-B from fluorescent lamps. A comparison of growth responses to solar radiation and temperature showed that the species that were most resistant to UV radiation grew fastest at higher temperatures. These data suggest that solar UV-B reduces the growth of fungi on the soil surface in the Antarctic terrestrial environment.

Effects of elevated ultraviolet radiation and endophytic fungi on plant growth and insect feeding in Lolium perenne, Festuca rubra, F. arundinacea and F. pratensis

Plants of perennial ryegrass (Lolium perenne L.), red fescue (Festuca rubra L.), tall fescue (F. arundinacea Schreb.) and meadow fescue (F. pratensis Huds) were exposed at an outdoor facility located in Edinburgh, UK to modulated levels of UV-B radiation (280-315 nm) using banks of cellulose diacetate filtered UV-B fluorescent lamps that also produce UV-A radiation (315-400 nm). The plants were derived from a single clone of each species and were grown both with and without colonization by naturally-occurring fungal endophytes. The UV-B treatment was a 30% elevation above the ambient erythemally-weighted level of UV-B during July to October. Growth of treated plants was compared with plants grown under elevated UV-A radiation alone produced by banks of polyester filtered lamps and with plants grown at ambient levels of solar radiation under banks of unenergized lamps. At the end of the treatment period, sample leaves were collected for feeding trials with the desert locust Schistocerca gregaria (Forsk). The UV-B treatment produced no effects on the aboveground biomass of any of the four grasses. The UV-B treatment and the UV-A control exposure both increased plant height and the number of daughter plants formed by rhizome growth in F. rubra. There were significant effects of endophyte presence on the total fresh and dry weights of F. arundinacea and F. rubra, on fresh weight only in F. pratensis, and on the fresh and dry weights of inflorescence in F. arundinacea and L. perenne. There were no effects of UV treatments on the absolute amounts of leaf consumed or on the feeding preferences of locusts for leaves with or without endophyte in three species: F. rubra, F. arundinacea and L. perenne. In F. pratensis there was no effect of UV treatment on the weight of leaves consumed but a significant UV x endophyte interaction caused by a marked change in feeding preference between leaves with and without endophyte that differed between the UV-B treatment and UV-A control exposures. The alkaloid compounds known as lolines were analysed in leaves of F. pratensis and were only found in plants grown with endophyte. However, there was no significant relationship between total loline content and insect feeding preference. These effects illustrate the potential complexities of species interactions under increasing levels of UV-B. The experiment also demonstrates the importance of appropriate controls in UV lamp supplementation experiments for interpretation of both plant growth and insect feeding effects.

Phialophora graminicola, a dark septate fungus, is a beneficial associate of the grass Vulpia ciliata ssp. ambigua

Seedlings of the annual grass Vulpia ciliata ssp. ambigua were grown in sterilized sand with a dark septate root fungus, Phialophora graminicola, which had been isolated from a natural population of the grass. Tiller number and shoot, root and total biomass of seedlings grown with P. graminicola were enhanced relative to uninoculated control plants in a growth room and a glasshouse experiment. Root length of seedlings grown with P. graminicola was significantly increased, but no effects of the fungus on root diameter, number of root hairs or specific root length were recorded. Root nitrogen content and shoot, root and total phosphorus contents of seedlings grown with the fungus were enhanced, but shoot nitrogen concentration of these plants was reduced. Shoot biomass and specific root length of inoculated plants were positively associated with the number of P. graminicola colonies re-isolated from roots. These data indicate that P. graminicola acts as a beneficial associate of V. ciliata ssp. ambigua seedlings under controlled conditions.

Effects of dry-deposited sulphur dioxide on fungal decomposition of angiosperm tree leaf litter III. Decomposition rates and fungal respiration

Ash (Fraxinus excelsior L.), birch (Betula spp.), hazel (Corylus avellana L.), sessile oak [Quercus petraea (Mattuschka) Liebl.] and sycamore (Acer pseudoplatanus L.) leaf litters from a virtually non-polluted and a heavily sulphur dioxide (SO₂ )-polluted woodland were fumigated with environmentally-realistic concentrations (0.010-0.030μl l^-1 ) of SO₂ for 16-68 wk in an open-air field-fumigation experiment. Fumigation inhibited the respiration (CO₂ evolution) and decomposition rates of the leaf litters. However, there were few differences in the responses between leaf litters from the two woodlands. In addition, pure cultures of four saprotrophic fungi were grown individually on irradiated hazel litter and exposed to c. 0.030μl l^-1 of gaseous SO² , for 28 d in the laboratory. The gas inhibited the respiration of Phoma exigua Desm. and Phoma macrostoma Mont, but not the respiration of Cladosporium cladosporioides (Fres.) de Vries or Coniothyrium quercinum Sacc. var. glandicola Grove. These results in part substantiated findings of previous experiments examining the effects of SO₂ on the structures of saprotrophic fungal communities. The effects of SO₂ on fungal decomposition of angiosperm tree leaf litter as possible causes of forest decline are discussed.

Effects of dry-deposited sulphur dioxide on fungal decomposition of angiosperm tree leaf litter II. Chemical content of leaf litters

Ash (Fraxinus excelsior L.), birch (Betula spp.), hazel (Corylus avellana L.), sessile oak [Quercus petraea (Mattuschka) Liebl.] and sycamore (Acer pseudoplatanus L.) leaf litters from a non-polluted and a heavily sulphur dioxide (SO₂ )-polluted woodland were fumigated with environmentally-realistic concentrations (0.010-0.030 μl l^-1 ) of SO₂ for 16-68 wk in an open-air field-fumigation experiment. Fumigation markedly increased sulphate and protons in leachates from the litters and decreased calcium and magnesium contents of the leaves. However, there were few differences in the responses between leaf litters from the two woodlands. This was attributed to rapid sulphate wash-out from the litters from the heavily polluted woodland, so that the litters from the two sites quickly reached the same sulphate status.

Effects of dry-deposited sulphur dioxide on fungal decomposition of angiosperm tree leaf litter I. Changes in communities of fungal saprotrophs

Comparisons of the saprotrophic fungi isolated from ash (Fraxinus excelsior L.), birch (Betula spp.), hazel (Corylus avellana L.), pedunculate oak (Quercus robur L.), sessile oak [Q. petraea (Mattuschka) Liebl.] and sycamore (Acer pseudoplatanus L.) leaf litters from three woodlands exposed to low, medium and high levels (c. 0.0→ 0.060μl l^-1 ) of sulphur dioxide (SO₂ ) showed that the composition of the fungal communities differed between sites. Fumigation of angiosperm tree leaf litters from the least and the most polluted site with environmentally-realistic concentrations (0.010-0.030 μl¹ ) of SO₂ for 16-68 wk in an open-air field-fumigation experiment resulted in marked changes in the composition of the fungal communities in the leaf litters, comparable with differences found between the woodland sites. Cladosporium spp., Epicoccutn nigrum Link, Fitsarium spp. and Phoma exigua Desm. were less commonly isolated from leaf litters exposed to SO² , whereas Coniothyrium quercinum Sacc. var. glandicola Grove, Cylindrocarpon orthosporum (Sacc.) Wollenw. and Penicillium spp. were more frequently isolated from fumigated litters. However, few differences could be detected in the response to SO₂ of the mycofloras of leaf litters originating from different woodland sites. In general, SO₂ did not affect the total extent of fungal occupancy of the microsites in the litter, as fungal species which decreased in abundance on exposure to the gas appeared to be replaced in the litter by other species more tolerant to the gas. SO₂ therefore appeared to be selectively toxic to saprotrophic fungi isolated from these litters.