Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya

Insights from cyanobacterial genomic and transcriptomic analyses into adaptation strategies in terrestrial environments

Phylogenomic analysis of Nostoc sp. MG11, a terrestrial cyanobacterium, and some terrestrial and freshwater Nostoc strains showed that the terrestrial strains grouped together in a distinctive clade, which reveals the effect of habitat on shaping Nostoc genomes. Terrestrial strains showed larger genomes and had higher predicted CDS contents than freshwater strains. Comparative genomic analysis demonstrated that genome expansion in the terrestrial Nostoc is supported by an increase in copy number of the core genes and acquisition of shared genes. Transcriptomic profiling analysis under desiccation stress revealed that Nostoc sp. MG11 protected its cell by induction of catalase, proteases, sucrose synthase, trehalose biosynthesis and maltodextrin utilization genes and maintained its normal metabolism during this condition by up-regulation of genes related to phycobilisomes and light reactions of photosynthesis, CO₂ fixation and protein metabolism. These results provide insights into the strategies related to survival and adaptation of Nostoc strains to terrestrial environments.

Phylogenetic insights into chroococcus-like taxa (Chroococcales, Cyanobacteria), describing Cryptochroococcus tibeticus gen. nov. sp. nov. and Limnococcus fonticola sp. nov. from Qinghai-Tibet plateau

Several coccoid cyanobacterial strains, morphologically similar to typical characteristics of Chroococcus, from the Qinghai-Tibet Plateau were isolated and characterized using a polyphasic approach including morphological and molecular information. Morphological characteristics, the phylogeny based on 16S rRNA gene, and 16S-23S internal transcribed spacer secondary structures support establishing a novel Chroococcus-like genus, Cryptochroococcus gen. nov., as well as Limnococcus fonticola sp. nov. Limnococcus is phylogenetically included in Chroococcaceae and has irregularly arranged thylakoids. Therefore, it should no longer be a member of Merismopediaceae (Synechococcales). The phylogeny based on the 16S rRNA gene revealed that Chroococcus-associated genera were monophyletic.

Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica

Recent microbiome research has shown that soil fertility, plant-associated microbiome, and crop production can be affected by abiotic environmental parameters. The effect of aridity gradient on rhizosphere-soil (rhizosphere) and endosphere-root (endosphere) prokaryotic structure and diversity associated with cacti remain poorly investigated and understood. In the current study, next-generation sequencing approaches were used to characterize the diversity and composition of bacteria and archaea associated with the rhizosphere and endosphere of Opuntia ficus-indica spineless cacti in four bioclimatic zones (humid, semi-arid, upper-arid, and lower-arid) in Tunisia. Our findings showed that bacterial and archaeal cactus microbiomes changed in inside and outside roots and along the aridity gradient. Plant compartment and aridity gradient were the influencing factors on the differentiation of microbial communities in rhizosphere and endosphere samples. The co-occurrence correlations between increased and decreased OTUs in rhizosphere and endosphere samples and soil parameters were determined according to the aridity gradient. Blastococcus, Geodermatophilus, Pseudonocardia, Promicromonospora, and Sphingomonas were identified as prevailing hubs and were considered as specific biomarkers taxa, which could play a crucial role on the aridity stress. Overall, our findings highlighted the prominence of the climatic aridity gradient on the equilibrium and diversity of microbial community composition in the rhizosphere and endosphere of cactus.

Microbial Ecology from the Himalayan Cryosphere Perspective

Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.

Alpine soil microbial ecology in a changing world

Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.

Macrochaete gen. nov. (Nostocales, Cyanobacteria), a taxon morphologically and molecularly distinct from Calothrix

Historically, the genus Calothrix included all noncolonial, tapered, heterocytous filaments within the cyanobacteria. However, recent molecular phylogenies show that "Calothrix" defined in this sense represents five distinct clades. The type species of Calothrix is marine, with solitary basal heterocytes, no akinetes, and distal ends tapering abruptly into short hairs. We examined the morphology and phylogeny of 45 tapering cyanobacteria in the Rivulariaceae, including freshwater and marine representatives of both Calothrix (35 strains) and its sister taxon Rivularia (10 strains). The marine Calothrix fall into two lineages, but we lack the generitype and so cannot identify the clade corresponding to the type species. The freshwater and soil Calothrix fall into the C. parietina clade and are characterized by having a basal heterocyte, no akinetes, and gradual tapering-but not into a long hyaline hair. Macrochaete gen. nov. is a freshwater taxon sister to the Calothrix lineages but clearly separated from Rivularia. The species in this genus differ morphologically from Calothrix by their ability to produce two heteromorphic basal heterocytes and specific secondary structures of the 16S-23S ITS. An additional feature present in most species is the presence of a distal, long hyaline hair, but this character has incomplete penetrance due to its expression only under specific environmental conditions (low phosphate), and in one species appears to be lost. We recognize three species: M. psychrophila (type species) from cold environments (high mountains, Antarctica), M. santannae from wet walls of subtropical South America, and M. lichenoides, a phycobiont of lichens from Europe.

Cyanobacterial diversity of western European biological soil crusts along a latitudinal gradient

Cyanobacteria associated with biological soil crusts (BSCs) have important attributes, such as nitrogen fixation and soil stabilisation. However, research on these organisms has been minimal, and their diversity and distribution throughout temperate Europe is currently unknown. The SCIN (Soil Crust International) project is a multidisciplinary research initiative that aims to achieve improved understanding of the BSCs of Europe, one facet being an investigation into the cyanobacterial communities of BSCs across a latitudinal gradient. Cyanobacteria assemblages were analysed by both morphological and molecular analysis. Two treatments were applied prior to DNA extraction, continued sample wetting and a dry sample process, and 16S ribosomal RNA (rRNA) amplicons were processed by Illumina MiSeq sequencing. The results reveal high and variable cyanobacterial diversity with each site showing a unique assemblage. Many common cyanobacterial genera, for example Nostoc and Microcoleus, were found in all sites but the abundances of different genera varied considerably. The polyphasic approach was found to be essential in recording the presence of important cyanobacteria that a single method itself did not highlight. The wet and dry treatments showed some differences in diversity, but mainly in abundance, this may suggest how cyanobacterial composition of BSCs changes with seasonal variability.

Investigating the diversity and community composition of cyanobacteria associated with biological soil crusts in climatically different regions of Europe.

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and sympatric Cacti species: Myrtillocactus geometrizans and Opuntia robusta. Phylogenetic profiling showed that the composition and assembly of microbial communities associated with Cacti were primarily influenced by the plant compartment; plant species, site, and season played only a minor role. Remarkably, bacterial, and archaeal diversity was higher in the phyllosphere than in the rhizosphere of Cacti, while the opposite was true for fungi. Semi-arid soils exhibited the highest levels of microbial diversity whereas the stem endosphere the lowest. Despite their taxonomic distance, M. geometrizans and O. robusta shared most microbial taxa in all analyzed compartments. Influence of the plant host did only play a larger role in the fungal communities of the stem endosphere. These results suggest that fungi establish specific interactions with their host plant inside the stem, whereas microbial communities in the other plant compartments may play similar functional roles in these two species. Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cacti holobiont. We envision this knowledge will help improve and sustain agriculture in arid and semi-arid regions of the world.