Angel Valverde

Microbial ecology of hot desert edaphic systems

A significant proportion of the Earths surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research.

Abiotic factors influence microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley

The McMurdo Dry Valleys collectively comprise the most extensive ice-free region in Antarctica and are considered one of the coldest arid environments on Earth. In low-altitude maritime-associated valleys, mineral soil profiles show distinct horizontal structuring, with a surface arid zone overlying a moist and biologically active zone generated by seasonally melted permafrost. In this study, long-term microenvironmental monitoring data show that temperature and soil humidity regimes vary in the soil horizons of north- and south-facing slopes within the Miers Valley, a maritime valley in the McMurdo Dry Valleys. We found that soil bacterial communities varied from the north to the south. The microbial assemblages at the surface and shallow subsurface depths displayed higher metabolic activity and diversity compared to the permafrost soil interface. Multivariate analysis indicated that K, C, Ca and moisture influenced the distribution and structure of microbial populations. Furthermore, because of the large % RH gradient between the frozen subsurface and the soil surface we propose that water transported to the surface as water vapour is available to microbial populations, either as a result of condensation processes or by direct adsorption from the vapour phase.

Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert

The Namib Desert is considered the oldest desert in the world and hyperarid for the last 5 million years. However, the environmental buffering provided by quartz and other translucent rocks supports extensive hypolithic microbial communities. In this study, open soil and hypolithic microbial communities have been investigated along an East–West transect characterized by an inverse fog-rainfall gradient. Multivariate analysis showed that structurally different microbial communities occur in soil and in hypolithic zones. Using variation partitioning, we found that hypolithic communities exhibited a fog-related distribution as indicated by the significant East–West clustering. Sodium content was also an important environmental factor affecting the composition of both soil and hypolithic microbial communities. Finally, although null models for patterns in microbial communities were not supported by experimental data, the amount of unexplained variation (68–97xa0%) suggests that stochastic processes also play a role in the assembly of such communities in the Namib Desert.

Evidence of species recruitment and development of hot desert hypolithic communities

Hypoliths, photosynthetic microbial assemblages found underneath translucent rocks, are widely distributed within the western region of the Namib Desert and other similar environments. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to assess the bacterial community structure of hypoliths and surrounding soil (below and adjacent to the hypolithic rock) at a fine scale (10u2009m radius). Multivariate analysis of T-RFs showed that hypolithic and soil communities were structurally distinct. T-RFLP-derived operational taxonomic units were linked to 16S rRNA gene clone libraries. Applying the ecological concept of indicator species, six and nine indicator lineages were identified for hypoliths and soil, respectively. Hypolithic communities were dominated by cyanobacteria affiliated to Pleurocapsales, whereas actinobacteria were prevalent in the soil. These results are consistent with the concept of species sorting and suggest that the bottom of the quartz rocks provides conditions suitable for the development of discrete and demonstrably different microbial assemblages. However, we found strong evidence for neutral assembly processes, as almost 90% of the taxa present in the hypoliths were also detected in the soil. These results suggest that hypolithons do not develop independently from microbial communities found in the surrounding soil, but selectively recruit from local populations.

Evidence for successional development in Antarctic hypolithic bacterial communities

Hypoliths (cryptic microbial assemblages that develop on the undersides of translucent rocks) are significant contributors to regional C and N budgets in both hot and cold deserts. Previous studies in the Dry Valleys of Eastern Antarctica have reported three morphologically distinct hypolithic community types: cyanobacteria dominated (type I), fungus dominated (type II) and moss dominated (type III). Here we present terminal-restriction fragment length polymorphism analyses to elucidate the bacterial community structure in hypolithons and the surrounding soils. We show clear and robust distinction in bacterial composition between bulk surface soils and hypolithons. Moreover, the bacterial assemblages were similar in types II and III hypolithons and clearly distinct from those found in type I. Through 16S rRNA gene 454 pyrosequencing, we show that Proteobacteria dominated all three types of hypolithic communities. As expected, Cyanobacteria were more abundant in type I hypolithons, whereas Actinobacteria were relatively more abundant in types II and III hypolithons, and were the dominant group in soils. Using a probabilistic dissimilarity metric and random sampling, we demonstrate that deterministic processes are more important in shaping the structure of the bacterial community found in types II and III hypolithons. Most notably, the data presented in this study suggest that hypolithic bacterial communities establish via a successional model, with the type I hypolithons acting as the basal development state.

Biogeography of bacterial communities in hot springs: a focus on the actinobacteria

Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5xa0°C and 5–10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.

Cyanobacteria drive community composition and functionality in rock-soil interface communities

Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T‐RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co‐occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules), and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.

Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica

Here we provide the first exploration of microbial diversity from three distinct Victoria Valley edaphic habitats, namely lithobionts (hypoliths, endoliths) and surface soils. Using a combination of terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene amplicon pyrosequencing we assess community structure and diversity patterns, respectively. Our analysis revealed that habitat type (endolithic versus hypolithic versus surface soils) significantly influenced bacterial community composition, even though dominant phyla such as Actinobacteria (41% of total reads) were common to all samples. Consistent with previous surveys in other Dry Valley ecosystems, we found that lithobionts were colonized by a few highly dominant phylotypes (such asGemmatimonasandLeptolyngbya). Our analyses also show that soil bacteria were more diverse and evenly distributed than initially expected based on previous evidence. In contrast to total bacteria, the distribution of Cyanobacteria was not strongly influenced by habitat type, although soil- and endolith-specific cyanobacterial lineages were found. The detection of cyanobacterial lineages in these habitats appears to be influenced by the dispersal of aquatic inocula from lacustrine communities or benthic mats which are abundant in Victoria Valley. Together, our results provide insights into the phylogenetic variation and community structure across niche habitats in Victoria Valley.

Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats

Polar Regions (continental Antarctica and the Arctic) are characterized by a range of extreme environmental conditions, which impose severe pressures on biological life. Polar cold-active cyanobacteria are uniquely adapted to withstand the environmental conditions of the high latitudes. These adaptations include high ultra-violet radiation and desiccation tolerance, and mechanisms to protect cells from freeze–thaw damage. As the most widely distributed photoautotrophs in these regions, cyanobacteria are likely the dominant contributors of critically essential ecosystem services, particularly carbon and nitrogen turnover in terrestrial polar habitats. These habitats include soils, permafrost, cryptic niches (including biological soil crusts, hypoliths and endoliths), ice and snow, and a range of aquatic habitats. Here we review current literature on the ecology, and the functional role played by cyanobacteria in various Arctic and Antarctic environments. We focus on the ecological importance of cyanobacterial communities in Polar Regions and assess what is known regarding the toxins they produce. We also review the responses and adaptations of cyanobacteria to extreme environments.

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil

Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few “species” (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small ‘core’ rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth.