Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic

Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica

Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.

Initial type and abundance of cyanobacteria determine morphotype development of phototrophic ecosystems

Phototrophic aggregates containing filamentous cyanobacteria occur naturally, for example, as cryoconite on glaciers and microbialites in fresh or marine waters, but their formation is not fully understood. Laboratory models are now available to reproduce aggregation, that is, the formation of different morphotypes like hemispheroids, microbial mats or sphere-like aggregates we call photogranules. In the model, activated sludge as starting matrix is transformed into aggregates enclosed by a phototrophic layer of growing cyanobacteria. These cyanobacteria were either enriched from the matrix or we added them intentionally. We hypothesize that the resulting morphotype depends on the type and concentration of the added cyanobacteria. When cyanobacteria from mature photogranules were added to activated sludge, photogranulation was not observed, but microbial mats were formed. Photogranulation of sludge could be promoted when adding sufficient quantities of cyanobacterial strains that form clumps when grown as isolates. The cyanobacteria putatively responsible for photogranulation were undetectable or only present in low abundance in the final communities of photogranules, which were always dominated by mat-forming cyanobacteria. We suggest that, in a temporal succession, the ecosystem engineer initiating photogranulation eventually disappears, leaving behind its structural legacy. We conclude that understanding phototrophic aggregate formation requires considering the initial succession stages of the ecosystem development.

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.

Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy

Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and terrestrial systems. Despite their well-known significance, their taxonomy remains problematic and is the subject of much research. Taxonomic issues of Cyanobacteria have consequently led to inaccurate curation within known reference databases, ultimately leading to problematic taxonomic assignment during diversity studies. Recent advances in sequencing technologies have increased our ability to characterize and understand microbial communities, leading to the generation of thousands of sequences that require taxonomic assignment. We herein propose CyanoSeq (https://zenodo.org/record/7569105), a database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. The taxonomy of CyanoSeq is based on the current state of cyanobacterial taxonomy, with ranks from the domain to genus level. Files are provided for use with common naive Bayes taxonomic classifiers, such as those included in DADA2 or the QIIME2 platform. Additionally, FASTA files are provided for creation of de novo phylogenetic trees with (near) full-length 16S rRNA gene sequences to determine the phylogenetic relationship of cyanobacterial strains and/or ASV/OTUs. The database currently consists of 5410 cyanobacterial 16S rRNA gene sequences along with 123 Chloroplast, Bacterial, and Vampirovibrionia (formally Melainabacteria) sequences.

Environmental micro-niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield

The pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50 m² area in the forefield of the Lobuche glacier (Himalayas, 5050 m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co-occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high-throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche-specific role of the micro-environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico-chemical and micro-climatic variations at the site-spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.

Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts)

The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or 'biocrusts'. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi-arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the first detailed description of Australia's biocrust microbiome assessed from 15 sites across the continent using 16S rRNA sequencing. The most abundant bacterial phyla from all sites were Cyanobacteria, Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Cyanobacterial communities from northern regions were more diverse and unclassified cyanobacteria were a noticeable feature of northern biocrusts. Segregation between northern and southern regions was largely due to the differential abundance of Microcoleus spp., with M. paludosus dominating in the north and M. vaginatus dominating in the south. The geographical shifts in bacterial composition and diversity were correlated to seasonal temperatures and summer rainfall. Our findings provide an initial reference for sampling strategies to maximize access to bacterial genetic diversity. As hubs for essential ecosystem services, further investigation into biocrusts in arid and semi-arid regions may yield discoveries of genetic mechanisms that combat increases in warming due to climate change.

Abundant and rare soil fungi exhibit distinct succession patterns in the forefield of Dongkemadi glacier on the central Qinghai-Tibet Plateau

Glaciers are retreating rapidly, exposing extensive new soil habitats in glacier forefields and providing unique areas for studying primary succession. However, understanding the variation patterns and assembly mechanisms of abundant and rare fungi subcommunities along the glacier-retreating chronosequence remains a knowledge gap, especially true for the vast Qinghai-Tibet Plateau (QTP). Here, we investigated fungal communities in the glacier forefield in Dongkemadi Glaicer on the central QTP. The results showed that fungal alpha diversity exhibited a clear increasing pattern in response to increasing of distance to glacier. The percentage of abundant OTUs decreased while the percentage of rare OTUs increased, suggesting that soil development is more beneficial to the rare taxa. The distributions of both abundant and rare subcommunities exhibited a clear spatial pattern along the distance to glacier, and might be strongly controlled by multiple environmental variables, including pH, soil moisture, vegetation status, soil organic carbon, total nitrogen, and soluble reactive phosphorus. Abundant and rare fungal subcommunities were structured in different assembly regimes. Dispersal limitation processes were dominant for both abundant and rare subcommunities but with a stronger contribution to abundant subcommunity assembly. Heterogeneous selection processes contributed higher and non-dominant processes contributed lower to abundant subcommunities than to rare subcommunities. The modular structure of the fungal co-occurrence network was highly localized along the soil chronosequence. By revealing distinct diversity patterns and community assembly mechanisms of abundant and rare fungal subcommunities, our study improved our understanding of ecological succession along the glacier-retreating chronosequence.

Diazotrophic activity and denitrification in two long-term chronosequences of maritime Antarctica

The main goals of this study were to identify whether key processes involved in microbial soil nitrogen transformations, such as diazotrophic activity and denitrification, the chemical properties of limiting elements in the soil, and microbial community structure, differ in the different successional stages of two long term chronosequences in maritime Antarctica. Moreover, we expect the rates of diazotrophic activity and denitrification to be stimulated by increases in air temperature and moisture. To answer these questions, we selected three stages in the succession (early, mid and late) in each of two well established chronosequences: three raised beaches in Ardley Island; and the Barton Peninsula, which includes two cosmogenically dated sites and the forefield of the Fourcade glacier. In the Ardley chronosequence, higher diazotrophic activity was found in the older successional stages, concomitant with an increase in the abundance of Cyanobacteria. In the Barton chronosequence, Cyanobacteria were only present and abundant (Microcoleus) in the early successional stage, coinciding with the highest diazotrophic activity. Denitrification in the Barton chronosequence tended to be highest at the mid successional sites, associated with the highest abundance of Rhodanobacter. In the Ardley chronosequence, the lowest abundance of Rhodanobacter was linked to lower denitrification rates in the mid successional stage. In the Ardley chronosequence, significant positive effects of passive warming and water addition on diazotrophic activity were detected in the first and the second years of the study respectively. In the Barton chronosequence on the other hand, there was no response to either passive warming or water addition, probably a manifestation of the higher nutrient limitation in this site. Denitrification showed no response to either warming or water addition. Thus, the response of microbial nitrogen transformations to global change is highly dependent on the environmental setting, such as soil origin, age and climate regime.

Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany

Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.

Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies

Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.

The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.

Disappearing Kilimanjaro snow-Are we the last generation to explore equatorial glacier biodiversity?

Glaciation accompanied our human ancestors in Africa throughout the Pleistocene. Regrettably, equatorial glaciers and snow are disappearing rapidly, and we are likely the last generation who will get to know these peculiar places. Despite the permanently harsh conditions of glacier/snow habitats, they support a remarkable diversity of life ranging from bacteria to animals. Numerous papers have been devoted to microbial communities and unique animals on polar glaciers and high mountains, but only two reports relate to glacial biodiversity in equatorial regions, which are destined to melt completely within the next few decades. Equatorial glaciers constitute "cold islands" in tropics, and discovering their diversity might shed light on the biogeography, dispersal, and history of psychrophiles. Thus, an opportunity to protect biota of equatorial glaciers hinges on ex situ conservation. It is timely and crucial that we should investigate the glacial biodiversity of the few remaining equatorial glaciers.

Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms

Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.

Strong in combination: Polyphasic approach enhances arguments for cold-assigned cyanobacterial endemism

Cyanobacteria of biological soil crusts (BSCs) represent an important part of circumpolar and Alpine ecosystems, serve as indicators for ecological condition and climate change, and function as ecosystem engineers by soil stabilization or carbon and nitrogen input. The characterization of cyanobacteria from both polar regions remains extremely important to understand geographic distribution patterns and community compositions. This study is the first of its kind revealing the efficiency of combining denaturing gradient gel electrophoresis (DGGE), light microscopy and culture‐based 16S rRNA gene sequencing, applied to polar and Alpine cyanobacteria dominated BSCs. This study aimed to show the living proportion of cyanobacteria as an extension to previously published meta‐transcriptome data of the same study sites. Molecular fingerprints showed a distinct clustering of cyanobacterial communities with a close relationship between Arctic and Alpine populations, which differed from those found in Antarctica. Species richness and diversity supported these results, which were also confirmed by microscopic investigations of living cyanobacteria from the BSCs. Isolate‐based sequencing corroborated these trends as cold biome clades were assigned, which included a potentially new Arctic clade of Oculatella. Thus, our results contribute to the debate regarding biogeography of cyanobacteria of cold biomes.