Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica

Vegetation drives the response of the active fraction of the rhizosphere microbial communities to soil warming in Antarctic vascular plants

In the Antarctic Peninsula, increases in mean annual temperature are associated with the coverage and population density of the two Antarctic vascular plant species-Deschampsia antarctica and Colobanthus quitensis-potentially modifying critical soil processes. In this study, we characterized the diversity and community composition of active microorganisms inhabiting the vascular plant rhizosphere in two sites with contrasting vegetation cover in King George Island, Western Antarctic Peninsula. We assessed the interplay between soil physicochemical properties and microbial diversity and composition, evaluating the effect of an in situ experimental warming on the microbial communities of the rhizosphere from D. antarctica and C. quitensis. Bacteria and Eukarya showed different responses to warming in both sites, and the effect was more noticeable in microbial eukaryotes from the low vegetation site. Furthermore, important changes were found in the relative abundance of Tepidisphaerales (Bacteria) and Ciliophora (Eukarya) between warming and control treatments. Our results showed that rhizosphere eukaryal communities are more sensitive to in situ warming than bacterial communities. Overall, our results indicate that vegetation drives the response of the active fraction of the microbial communities from the rhizosphere of Antarctic vascular plants to soil warming.

Source and acquisition of rhizosphere microbes in Antarctic vascular plants

Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.

Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems

Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.

Ecology and potential functions of plant-associated microbial communities in cold environments

Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.

Interaction between bacterial endophytes and host plants

Endophytic bacteria are mainly present in the plant's root systems. Endophytic bacteria improve plant health and are sometimes necessary to fight against adverse conditions. There is an increasing trend for the use of bacterial endophytes as bio-fertilizers. However, new challenges are also arising regarding the management of these newly discovered bacterial endophytes. Plant growth-promoting bacterial endophytes exist in a wide host range as part of their microbiome, and are proven to exhibit positive effects on plant growth. Endophytic bacterial communities within plant hosts are dynamic and affected by abiotic/biotic factors such as soil conditions, geographical distribution, climate, plant species, and plant-microbe interaction at a large scale. Therefore, there is a need to evaluate the mechanism of bacterial endophytes' interaction with plants under field conditions before their application. Bacterial endophytes have both beneficial and harmful impacts on plants but the exact mechanism of interaction is poorly understood. A basic approach to exploit the potential genetic elements involved in an endophytic lifestyle is to compare the genomes of rhizospheric plant growth-promoting bacteria with endophytic bacteria. In this mini-review, we will be focused to characterize the genetic diversity and dynamics of endophyte interaction in different host plants.

Fighting plant pathogens with cold-active microorganisms: biopesticide development and agriculture intensification in cold climates

Cold-adapted (CA) microorganisms (= psychrophiles or psychrotolerants) are key players of many ecological interactions in natural ecosystems. Some of them can colonize the rhizosphere of plants and cause damage to their hosts; others, on the contrary, protect plants from their pathogens through direct and indirect mechanisms, thus promoting plant growth and development. These "protective" microbes are known as biocontrol agents (BCA). BCA either limit or inhibit the growth of plant pathogens, owing to the excretion of a panoply of secondary metabolites (including soluble and volatile antibiotics, siderophores, quorum sensing interfering agents). BCA can also control plant pathogens through indirect mechanisms, including competence for nutrients and space, or else by interfering with their chemical communication. That explains why some of these BCA have been included in the formulation of commercial biopesticides, which are environmentally friendly products containing live cells used to control plant diseases and pests. At present, the development of biopesticides from mesophilic microorganisms is an established technology. Unfortunately, these biopesticides are not active at low temperatures. On the other hand, the information concerning the potential use of CA-BCA for the same goal is at its infancy. Here, we review the current knowledge concerning the isolation, identification, and characterization of CA microbes which act as antagonists of plant pathogens, including the mechanisms they deploy to antagonize plant pathogens. We also illustrate their biotechnological potential to develop CA biopesticides and discuss their utility in the context of mountainous agriculture. KEY POINTS: • Many naturally occurring cold-active microbes antagonize plant pathogens. • The mechanisms of biocontrol exerted by these microbes are either direct or indirect. • Cold-active biocontrol agents can be used to develop biopesticides. • Cold-active biopesticides are crucial for sustainably intensifying agriculture in cold climates.

Occurrence of Soil Fungi in Antarctic Pristine Environments

The presence of fungi in pristine Antarctic soils is of particular interest because of the diversity of this microbial group. However, the extreme conditions that coexist in Antarctica produce a strong selective pressure that could lead to the evolution of novel mechanisms for stress tolerance by indigenous microorganisms. For this reason, in recent years, research on cold-adapted microorganisms has increased, driven by their potential value for applications in biotechnology. Cold-adapted fungi, in particular, have become important sources for the discovery of novel bioactive secondary metabolites and enzymes. In this study, we studied the fungal community structure of 12 soil samples from Antarctic sites, including King George Island (including Collins Glacier), Deception Island and Robert Island. Culturable fungi were isolated and described according to their morphological and phenotypical characteristics, and the richness index was compared with soil chemical properties to describe the fungal community and associated environmental parameters. We isolated 54 fungal strains belonging to the following 19 genera: Penicillium, Pseudogymnoascus, Lambertella, Cadophora, Candida, Mortierella, Oxygenales, Geomyces, Vishniacozyma, Talaromyces, Rhizopus, Antarctomyces, Cosmospora, Tetracladium, Leptosphaeria, Lecanicillium, Thelebolus, Bjerkandera and an uncultured Zygomycete. The isolated fungi were comprised of 70% Ascomycota, 10% Zygomycota, 10% Basidiomycota, 5% Deuteromycota and 5% Mucoromycota, highlighting that most strains were associated with similar genera grown in cold environments. Among the culturable strains, 55% were psychrotrophic and 45% were psychrophilic, and most were Ascomycetes occurring in their teleomorph forms. Soils from the Collins Glacier showed less species richness and greater species dominance compared with the rest of the sites, whereas samples 4, 7, and 10 (from Fildes Bay, Coppermine Peninsula and Arctowski Station, respectively) showed greater species richness and less species dominance. Species richness was related to the C/N ratio, whereas species dominance was inversely related to C and N content. Thus, the structure of the fungal community was mainly related to soil chemical parameters more than sample location and altitude.

Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica

Seabirds and pinnipeds play an important role in biogeochemical cycling by transferring nutrients from aquatic to terrestrial environments. Indeed, soils rich in animal depositions have generally high organic carbon, nitrogen and phosphorus contents. Several studies have assessed bacterial diversity in Antarctic soils influenced by marine animals; however most have been conducted in areas with significant human impact. Thus, we chose Cape Shirreff, Livingston Island, an Antarctic Specially Protected Area designated mainly to protect the diversity of marine vertebrate fauna, and selected sampling sites with different types of animals coexisting in a relatively small space, and where human presence and impact are negligible. Using 16S rRNA gene analyses through massive sequencing, we assessed the influence of animal concentrations, via their modification of edaphic characteristics, on soil bacterial diversity and composition. The nutrient composition of soils impacted by Antarctic fur seals and kelp gulls was more similar to that of control soils (i.e. soils without visible presence of plants or animals), which may be due to the more active behaviour of these marine animals compared to other species. Conversely, the soils from concentrations of southern elephant seals and penguins showed greater differences in soil nutrients compared to the control. In agreement with this, the bacterial communities of the soils associated with these animals were most different from those of the control soils, with the soils of penguin colonies also possessing the lowest bacterial diversity. However, all the soils influenced by the presence of marine animals were dominated by bacteria belonging to Gammaproteobacteria, particularly those of the genus Rhodanobacter. Therefore, we conclude that the modification of soil nutrient composition by marine vertebrates promotes specific groups of bacteria, which could play an important role in the recycling of nutrients in terrestrial Antarctic ecosystems.

Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments

Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal communities from extreme environments collected at Aldmiralty Bay (Antarctica). A total of 891 and 226 isolates was obtained from soil and marine sediment samples, respectively. The most abundant isolates from soil samples were representatives of the genera Leucosporidium, Pseudogymnoascus, and a non-identified Ascomycota NIA6. Metschnikowia sp. was the most abundant taxon from marine samples, followed by isolates from the genera Penicillium and Pseudogymnoascus. Many of the genera were exclusive in marine sediment or terrestrial samples. However, representatives of eight genera were found in both types of samples. Data from non-metric multidimensional scaling showed that each sampling site is unique in their physical-chemical composition and fungal community. Biotechnological potential in relation to enzymatic production at low/moderate temperatures was also investigated. Ligninolytic enzymes were produced by few isolates from root-associated soil. Among the fungi isolated from marine sediments, 16 yeasts and nine fungi showed lipase activity and three yeasts and six filamentous fungi protease activity. The present study permitted increasing our knowledge on the diversity of fungi that inhabit the Antarctic, finding genera that have never been reported in this environment before and discovering putative new species of fungi.

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils

Expansion of penguin activity in maritime Antarctica, under ice thaw, increases the chances of penguin feces affecting soil microbiomes. The detail of such effects begins to be revealed. By comparing soil geochemistry and microbiome composition inside (one site) and outside (three sites) of the rookery, we found significant effects of penguin feces on both. First, penguin feces change soil geochemistry, causing increased moisture content (MC) of ornithogenic soils and nutrients C, N, P, and Si in the rookery compared to non-rookery sites, but not pH. Second, penguin feces directly affect microbiome composition in the rookery, not those outside. Specifically, we found 4,364 operational taxonomical units (OTUs) in 404 genera in six main phyla: Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, Chloroflexi, and Bacteroidetes. Although the diversity is similar among the four sites, the composition is different. For example, penguin rookery has a lower abundance of Acidobacteria, Chloroflexi, and Nitrospirae but a higher abundance of Bacteroidetes, Firmicutes, and Thermomicrobia. Strikingly, the family Clostridiaceae of Firmicutes of penguin-feces origin is most abundant in the rookery than non-rookery sites with two most abundant genera, Tissierella and Proteiniclasticum. Redundancy analysis showed all measured geochemical factors are significant in structuring microbiomes, with MC showing the highest correlation. We further extracted 21 subnetworks of microbes which contain 4,318 of the 4,364 OTUs using network analysis and are closely correlated with all geochemical factors except pH. Our finding f penguin feces, directly and indirectly, affects soil microbiome suggests an important role of penguins in soil geochemistry and microbiome structure of maritime Antarctica.

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.