The Bacterial Microbiome Associated With Arid Biocrusts and the Biogeochemical Influence of Biocrusts Upon the Underlying Soil

Isolation of biocrust cyanobacteria and evaluation of Cu, Pb, and Zn immobilisation potential for soil restoration and sustainable agriculture

Soil contamination by heavy metals represents an important environmental and public health problem of global concern. Biocrust-forming cyanobacteria offer promise for heavy metal immobilisation in contaminated soils due to their unique characteristics, including their ability to grow in contaminated soils and produce exopolysaccharides (EPS). However, limited research has analysed the representativeness of cyanobacteria in metal-contaminated soils. Additionally, there is a lack of studies examining how cyanobacteria adaptation to specific environments can impact their metal-binding capacity. To address this research gap, we conducted a study analysing the bacterial communities of cyanobacteria-dominated biocrusts in a contaminated area from South Sardinia (Italy). Additionally, by using two distinct approaches, we isolated three Nostoc commune strains from cyanobacteria-dominated biocrust and we also evaluated their potential to immobilise heavy metals. The first isolation method involved acclimatizing biocrust samples in liquid medium while, in the second method, biocrust samples were directly seeded onto agar plates. The microbial community analysis revealed Cyanobacteria, Bacteroidota, Proteobacteria, and Actinobacteria as the predominant groups, with cyanobacteria representing between 13.3 % and 26.0 % of the total community. Despite belonging to the same species, these strains exhibited different growth rates (1.1-2.2 g L-1 of biomass) and capacities for EPS production (400-1786 mg L-1). The three strains demonstrated a notable ability for metal immobilisation, removing up to 88.9 % of Cu, 86.2 % of Pb, and 45.3 % of Zn from liquid medium. Cyanobacteria EPS production showed a strong correlation with the removal of Cu, indicating its role in facilitating metal immobilisation. Furthermore, differences in Pb immobilisation (40-86.2 %) suggest possible environmental adaptation mechanisms of the strains. This study highlights the promising application of N. commune strains for metal immobilisation in soils, offering a potential bioremediation tool to combat the adverse effects of soil contamination and promote environmental sustainability.

A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities

Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as Bacillus, Paenibacillus, and Pseudomonas. Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.

Engineering highly productive cyanobacteria towards carbon negative emissions technologies

Cyanobacteria are a diverse and ecologically important group of photosynthetic prokaryotes that contribute significantly to the global carbon cycle through the capture of CO2 as biomass. Cyanobacterial biotechnology could play a key role in a sustainable bioeconomy through negative emissions technologies (NETs), such as carbon sequestration or bioproduction. However, the primary issues of low productivities and high infrastructure costs currently limit the commercialisation of such applications. The isolation of several fast-growing strains and recent advancements in molecular biology tools now offer promising new avenues for improving yields, including metabolic engineering approaches guided by high-throughput screening and metabolic models. Furthermore, emerging research on engineering coculture communities could help to develop more robust culturing systems to support broader NET applications.

Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops

Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared a similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared with those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All of the examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared with the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence the bacterial and diazotrophic community composition of any of these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced the community composition and function of these biocrusts.

Environmental conditions play a key role in controlling the composition and diversity of Colombian biocrust microbiomes

Drylands soils worldwide are naturally colonized by microbial communities known as biocrusts. These soil microbiomes render important ecosystem services associated with soil fertility, water holding capacity, and stability to the areas they cover. Because of the importance of biocrusts in the global cycling of nutrients, there is a growing interest in describing the many microbial configurations these communities display worldwide. However, comprehensive 16S rRNA genes surveys of biocrust communities do not exist for much of the planet: for example, in the continents of South America and the northern part of Africa. The absence of a global understanding of biocrust biodiversity has lead us to assign a general importance to community members that may, in fact, be regional. Here we report for the first time the presence of biocrusts in Colombia (South America) through 16S rRNA genes surveys across an arid, a semi-arid and a dry subtropical region within the country. Our results constitute the first glance of the Bacterial/Archaeal communities associated with South American biocrust microbiomes. Communities where cyanobacteria other than Microcoleus vaginatus prevail, despite the latter being considered a key species elsewhere, illustrate differentiable results in these surveys. We also find that the coastal biocrust communities in Colombia include halo-tolerant and halophilic species, and that niche preference of some nitrogen fixing organisms deviate from previously described global trends. In addition, we identified a high proportion (ranging from 5 to 70%, in average) of cyanobacterial sequences that did not match any formally described cyanobacterial species. Our investigation of Colombian biocrusts points to highly diverse communities with climatic regions controlling taxonomic configurations. They also highlight an extensive local diversity to be discovered which is central to better design management and restoration strategies for drylands soils currently undergoing disturbances due to land use and global warming. Finally, this field study highlights the need for an improved mechanistic understanding of the response of key biocrust community members to changes in moisture and temperature.

Changes in Microbial Composition During the Succession of Biological Soil Crusts in Alpine Hulun Buir Sandy Land, China

Biological soil crusts (biocrusts) are considered "desert ecosystem engineers" because they play a vital role in the restoration and stability maintenance of deserts, including those cold sandy land ecosystems at high latitudes, which are especially understudied. Microorganisms participate in the formation and succession of biocrusts, contributing to soil properties' improvement and the stability of soil aggregates, and thus vegetation development. Accordingly, understanding the composition and successional characteristics of microorganisms is a prerequisite for analyzing the ecological functions of biocrusts and related applications. Here, the Hulun Buir Sandy Land region in northeastern China-lying at the highest latitude of any sandy land in the country-was selected for study. Through a field investigation and next-generation sequencing (Illumina MiSeq PE300 Platform), our goal was to assess the shifts in diversity and community composition of soil bacteria and fungi across different stages during the succession of biocrusts in this region, and to uncover the main factors involved in shaping their soil microbial community. The results revealed that the nutrient enrichment capacity of biocrusts for available nitrogen, total nitrogen, total phosphorus, total content of water-soluble salt, available potassium, soil organic matter, and available phosphorus was progressively enhanced by the succession of cyanobacterial crusts to lichen crusts and then to moss crusts. In tandem, soil bacterial diversity increased as biocrust succession proceeded but fungal diversity decreased. A total of 32 bacterial phyla and 11 fungal phyla were identified, these also known to occur in other desert ecosystems. Among those taxa, the relative abundance of Proteobacteria and Cyanobacteria significantly increased and decreased, respectively, along the cyanobacterial crust-lichen-moss crust successional gradient. However, for Actinobacteria, Chloroflexi, and Acidobacteria their changed relative abundance was significantly hump-shaped, increasing in the shift from cyanobacterial crust to lichen crust, and then decreasing as lichen crust shifted to moss crust. In this process, the improved soil properties effectively enhanced soil bacterial and fungal community composition. Altogether, these findings broaden our understanding about how soil microbial properties can change during the succession of biocrusts in high-latitude, cold sandy land ecosystems.

Co-cultures from Plants and Cyanobacteria: A New Way for Production Systems in Agriculture and Bioprocess Engineering

Due to the global increase in the world population, it is not possible to ensure a sufficient food supply without additional nitrogen input into the soil. About 30-50% of agricultural yields are due to the use of chemical fertilizers in modern times. However, overfertilization threatens biodiversity, such as nitrogen-loving, fast-growing species overgrow others. The production of artificial fertilizers produces nitrogen oxides, which act as greenhouse gases. In addition, overfertilization of fields also releases ammonia, which damages surface waters through acidification and eutrophication. Diazotrophic cyanobacteria, which usually form a natural, stable biofilm, can fix nitrogen from the atmosphere and release it into the environment. Thus, they could provide an alternative to artificial fertilizers. In addition to this, biofilms stabilize soils and thus protect against soil erosion and desiccation. This chapter deals with the potential of cyanobacteria as the use of natural fertilizer is described. Possible partners such as plants and callus cells and the advantages of artificial co-cultivation will be discussed later. In addition, different cultivation systems for studying artificial co-cultures will be presented. Finally, the potential of artificial co-cultures in the agar industry will be discussed.

The Microbiology of Biological Soil Crusts

Biological soil crusts are thin, inconspicuous communities along the soil atmosphere ecotone that, until recently, were unrecognized by ecologists and even more so by microbiologists. In its broadest meaning, the term biological soil crust (or biocrust) encompasses a variety of communities that develop on soil surfaces and are powered by photosynthetic primary producers other than higher plants: cyanobacteria, microalgae, and cryptogams like lichens and mosses. Arid land biocrusts are the most studied, but biocrusts also exist in other settings where plant development is constrained. The minimal requirement is that light impinge directly on the soil; this is impeded by the accumulation of plant litter where plants abound. Since scientists started paying attention, much has been learned about their microbial communities, their composition, ecological extent, and biogeochemical roles, about how they alter the physical behavior of soils, and even how they inform an understanding of early life on land. This has opened new avenues for ecological restoration and agriculture.

Bio-Characterization and Liquid Chromatography-Mass Spectrometry Analysis of Exopolysaccharides in Biofilm-Producing Cyanobacteria Isolated from Soil Crust: Exploring the Potential of Microalgal Biomolecules

Exopolysaccharide-producing cyanobacterial strains in biological soil crusts are described, in addition to their chemical properties and antioxidant and flocculation activities. The EPSs from Pudukkottai blackish biological soil crusts (PBBSCs) showed significant amounts of total soluble proteins (0.1687 mg/mL) and carbohydrates (0.8056 mg/mL) compared with the Ariyalur blackish biological soil crusts (ABBSCs). LC-MS analysis of the cyanobacterial polysaccharides revealed the presence of natural sugars such as ribose and glucose/mannose, and uronic acids. The FTIR spectrum showed specific peak for OH and -NH stretching, C-H stretching, and carboxylic acids as the dominant groups in EPS. The in vitro DPPH assay of EPSs from PBBSCs showed 74.3% scavenging activity. Furthermore, the reducing power was determined to be 0.59 ata 500 mg/mL concentration, respectively. The extracted EPSs from the biological soil crust flocculated Kaolin clay suspension maximum at 500 mg/mL. Consequently, the cyanobacterial strain and exopolysaccharide characterization from the sacred forest's biological soil crust were analyzed for their bioactive potential, bio-crust diversity, and distribution.

Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert

Introduction

Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert.

Methods

This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity.

Results

Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (p ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations.

Discussion

Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.

Protist Diversity Responses to Experimental N Deposition in Biological Crusts of a Semiarid Mediterranean Ecosystem

Biological soil crusts (BSC) are associations of different macro and microorganisms and aggregated soil particles located on the surface of soils in many different habitats. BSC harbour a diverse and complex community of ciliates and testate amoebae. These phagotrophic protists play an important role in C and N recycling in soil ecosystems but have not been frequently studied in BSC. In this context, the effects of three increasing N inputs on ciliates and testate amoebae in crusts from a semi-arid Mediterranean ecosystem were evaluated. A field experiment with artificial N-deposition was designed to mimic the effects caused by anthropogenic N depositions. The results have shown that the protist populations of these semi-arid Mediterranean environments have lower species richness than other soil environments. The increase in N produces a net loss of diversity in the populations studied and shifts in the community structure. It has also been shown that some ciliates and testate amoebae, due to their population responses to increased N concentrations, could potentially be used as bio-indicators of N contamination in these BSCs.

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.

Chronicle of Research into Lichen-Associated Bacteria

Lichens are mutually symbiotic systems consisting of fungal and algal symbionts. While diverse lichen-forming fungal species are known, limited species of algae form lichens. Plasticity in the combination of fungal and algal species with different eco-physiological properties may contribute to the worldwide distribution of lichens, even in extreme habitats. Lichens have been studied systematically for more than 200 years; however, plasticity in fungal-algal/cyanobacterial symbiotic combinations is still unclear. In addition, the association between non-cyanobacterial bacteria and lichens has attracted attention in recent years. The types, diversity, and functions of lichen-associated bacteria have been studied using both culture-based and culture-independent methods. This review summarizes the history of systematic research on lichens and lichen-associated bacteria and provides insights into the current status of research in this field.

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems. IMPORTANCE Biocrusts serve as a keystone element of desert and dryland ecosystems, stabilizing soils, retaining moisture, and serving as a carbon and nitrogen source in oligotrophic environments. Biocrusts cover approximately 12% of the Earth's terrestrial surface but are threatened by climate change and anthropogenic disturbance. Given their keystone role in ecosystem functioning, loss will have wide-spread consequences. Biocrust microbial constituents must withstand polyextreme environmental conditions including high UV exposure, desiccation, oligotrophic conditions, and temperature fluctuations over short time scales. By comparing biocrust communities with co-occurring hypolithic communities (which inhabit the ventral sides of semitranslucent stones and are buffered from environmental extremes), we identified traits that are likely key adaptations to extreme conditions. These include DNA damage repair, environmental sensing and response, and intracellular competition. Comparison of the two niches, which differ primarily in exposure levels to extreme conditions, makes this system ideal for understanding how functional traits are structured by the environment.

Microbial Communities in Biocrusts Are Recruited From the Neighboring Sand at Coastal Dunes Along the Baltic Sea

Biological soil crusts occur worldwide as pioneer communities stabilizing the soil surface. In coastal primary sand dunes, vascular plants cannot sustain due to scarce nutrients and the low-water-holding capacity of the sand sediment. Thus, besides planted dune grass, biocrusts are the only vegetation there. Although biocrusts can reach high coverage rates in coastal sand dunes, studies about their biodiversity are rare. Here, we present a comprehensive overview of the biodiversity of microorganisms in such biocrusts and the neighboring sand from sampling sites along the Baltic Sea coast. The biodiversity of Bacteria, Cyanobacteria, Fungi, and other microbial Eukaryota were assessed using high-throughput sequencing (HTS) with a mixture of universal and group-specific primers. The results showed that the biocrusts recruit their microorganisms mainly from the neighboring sand rather than supporting a universal biocrust microbiome. Although in biocrusts the taxa richness was lower than in sand, five times more co-occurrences were identified using network analysis. This study showed that by comparing neighboring bare surface substrates with biocrusts holds the potential to better understand biocrust development. In addition, the target sequencing approach helps outline potential biotic interactions between different microorganisms groups and identify key players during biocrust development.

Responses of Biocrust and Associated Soil Bacteria to Novel Climates Are Not Tightly Coupled

Climate change is expanding drylands even as land use practices degrade them. Representing ∼40% of Earth’s terrestrial surface, drylands rely on biological soil crusts (biocrusts) for key ecosystem functions including soil stability, biogeochemical cycling, and water capture. Understanding how biocrusts adapt to climate change is critical to understanding how dryland ecosystems will function with altered climate. We investigated the sensitivity of biocrusts to experimentally imposed novel climates to track changes in productivity and stability under both warming and cooling scenarios. We established three common gardens along an elevational-climate gradient on the Colorado Plateau. Mature biocrusts were collected from each site and reciprocally transplanted intact. Over 20 months we monitored visible species composition and cover, chlorophyll a, and the composition of soil bacterial communities using high throughput sequencing. We hypothesized that biocrusts replanted at their home site would show local preference, and biocrusts transplanted to novel environments would maintain higher cover and stability at elevations higher than their origin, compared to at elevations lower than their origin. We expected responses of the visible biocrust cover and soil bacterial components of the biocrust community to be coupled, with later successional taxa showing higher sensitivity to novel environments. Only high elevation sourced biocrusts maintained higher biocrust cover and community stability at their site of origin. Biocrusts from all sources had higher cover and stability in the high elevation garden. Later successional taxa decreased cover in low elevation gardens, suggesting successional reversal with warming. Visible community composition was influenced by both source and transplant environment. In contrast, soil bacterial community composition was not influenced by transplant environments but retained fidelity to the source. Thus, responses of the visible and soil bacterial components of the biocrust community were not coupled. Synthesis: Our results suggest biocrust communities are sensitive to climate change, and loss of species and function can be expected, while associated soil bacteria may be buffered against rapid change.

From Rags to Enriched: Metagenomic Insights into Ammonia-oxidizing Archaea Following Ammonia Enrichment of a Denuded Oligotrophic Soil Ecosystem

Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavorable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in-silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia oxidizing archaea (AOA) can be considered as the one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates. This article is protected by copyright. All rights reserved.

Biological Soil Crust From Mesic Forests Promote a Specific Bacteria Community

Biological soil crusts (biocrusts) harbor a diverse community of various microorganisms with microalgae as primary producers and bacteria living in close association. In mesic regions, biocrusts emerge rapidly on disturbed surface soil in forest, typically after clear-cut or windfall. It is unclear whether the bacterial community in biocrusts is similar to the community of the surrounding soil or if biocrust formation promotes a specific bacterial community. Also, many of the interactions between bacteria and algae in biocrusts are largely unknown. Through high-throughput-sequencing analysis of the bacterial community composition, correlated drivers, and the interpretation of biological interactions in a biocrust of a forest ecosystem, we show that the bacterial community in the biocrust represents a subset of the community of the neighboring soil. Bacterial families connected with degradation of large carbon molecules, like cellulose and chitin, and the bacterivore Bdellovibrio were more abundant in the biocrust compared to bulk soil. This points to a closer interaction and nutrient recycling in the biocrust compared to bulk soil. Furthermore, the bacterial richness was positively correlated with the content of mucilage producing algae. The bacteria likely profit from the mucilage sheaths of the algae, either as a carbon source or protectant from grazing or desiccation. Comparative sequence analyses revealed pronounced differences between the biocrust bacterial microbiome. It seems that the bacterial community of the biocrust is recruited from the local soil, resulting in specific bacterial communities in different geographic regions.

Coleofasciculaceae, a Monophyletic Home for the Microcoleus steenstrupii Complex and Other Desiccation-tolerant Filamentous Cyanobacteria

Cyanobacteria classified as Microcoleus steenstrupii play a significant role as pioneers of biological soil crusts (biocrusts), but this taxon is recognized to constitute a diverse complex of strains and field populations. With the aim of clarifying its systematics, we conducted a polyphasic characterization of this and allied taxa. A 16S ribosomal gene meta-analysis of published environmental sequences showed that the complex encompasses a variety of well supported genus-level clades with clade-specific environmental preferences, indicating significant niche differentiation. Fifteen strains in the M. steenstrupii complex were selected as representative of naturally occurring clades and studied using 16S rRNA gene phylogeny, morphology, and niche delineation with respect to temperature and rainfall. Bayesian phylogenetic reconstructions within a comprehensive, curated database of long 16S rRNA cyanobacterial sequences (1,000 base pairs or more) showed that they all belonged in a monophyletic, family-level clade (91.4% similarity) that included some other known genera of desiccation-resistant, largely terrestrial, filamentous, nonheterocystous cyanobacteria, including Coleofasciculus, the type genus for the family Coleofasciculaceae. To accommodate this biodiversity, we redescribe the Coleofasciculaceae, now composed of 11 genera, among which six are newly described herein (Funiculus, Parifilum, Arizonema, Crassifilum, Crustifilum, and Allocoleopsis), and five were previously recognized (Porphyrosiphon, Coleofasciculus, Pycnacronema, Potamolinea, and Wilmottia). We provide an evaluation of their respective niches and global distributions within biocrusts based on published molecular data. This new systematics treatment should help simplify and improve our understanding of the biology of terrestrial cyanobacteria.

Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran

Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole-genome sequences (3.94 X) of an approximately 1600-year-old naturally mummified sheep recovered from Chehrābād, a salt mine in northwestern Iran. Comparative analyses of published ancient sequences revealed the remarkable DNA integrity of this mummy. Hallmarks of postmortem damage, fragmentation and hydrolytic deamination are substantially reduced, likely owing to the high salinity of this taphonomic environment. Metagenomic analyses reflect the profound influence of high-salt content on decomposition; its microbial profile is predominated by halophilic archaea and bacteria, possibly contributing to the remarkable preservation of the sample. Applying population genomic analyses, we find clustering of this sheep with Southwest Asian modern breeds, suggesting ancestry continuity. Genotyping of a locus influencing the woolly phenotype showed the presence of an ancestral 'hairy' allele, consistent with hair fibre imaging. This, along with derived alleles associated with the fat-tail phenotype, provides genetic evidence that Sasanian-period Iranians maintained specialized sheep flocks for different uses, with the 'hairy', 'fat-tailed'-genotyped sheep likely kept by the rural community of Chehrābād's miners.

In-situ soil greenhouse gas fluxes under different cryptogamic covers in maritime Antarctica

Soils can influence climate by sequestering or emitting greenhouse gases (GHG) such as carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). We are far from understanding the direct influence of cryptogamic covers on soil GHG fluxes, particularly in areas free of potential anthropogenic confounding factors. We assessed the role of well-developed cryptogamic covers in soil attributes, as well as in the in-situ exchange of GHG between Antarctic soils and the atmosphere during the austral summer. We found lower values of soil organic matter, total organic carbon, and total nitrogen in bare areas than in soils covered by mosses and, particularly, lichens. These differences, together with concomitant decreases and increases in soil temperature and moisture, respectively, resulted in increases in in-situ CO₂ emission (i.e. ecosystem respiration) and decreases in CH₄ uptake but no significant changes in N₂O fluxes. We found consistent linear positive and negative relationships between soil attributes (i.e. soil organic matter, total organic carbon and total nitrogen) and CO₂ emissions and CH₄ uptake, respectively, and polynomial relationships between these soil attributes and net N₂O fluxes. Our results indicate that any increase in the area occupied by cryptogams in terrestrial Antarctic ecosystems (due to increased growing season and increasingly warming conditions) will likely result in parallel increases in soil fertility as well as in an enhanced capacity to emit CO₂ and a decreased capacity to uptake CH₄. Such changes, unless offset by parallel C uptake processes, would represent a paradigmatic example of a positive climate change feedback. Further, we show that the fate of these terrestrial ecosystems under future climate scenarios, as well as their capacity to exchange GHG with the atmosphere might depend on the relative ability of different aboveground cryptogams to thrive under the new conditions.

Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem

Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.

Cryptogamic cover determines soil attributes and functioning in polar terrestrial ecosystems

We still lack studies that provide evidence for direct links between the development of soil surface cryptogamic communities and soil attributes and functioning. This is particularly true in areas free of potentially confounding factors such as different soil types, land uses, or anthropogenic disturbances. Despite the ecological importance of polar ecosystems and their sensitivity to climate change, we are far from understanding how their soils function and will respond to climate change-driven alterations in above- and belowground features. We used two complementary approaches (i.e. cover gradients in the forefront of retreating glaciers as well as long-time deglaciated areas with well-developed cryptogamic cover types) to evaluate the role of cryptogams driving multiple soil biotic and abiotic attributes and functioning rates in polar terrestrial ecosystems. Increases in cryptogamic cover were consistently related to increases in organic matter accumulation, soil fertility, and bacterial diversity, but also in enhanced soil functioning rates in both sampling areas. However, we also show that the ability to influence soil attributes varies among different polar cryptogamic covers, indicating that their differential ability to thrive under climate-change scenarios will largely determine the fate of polar soils in coming decades.

Insights into dryland biocrust microbiome: geography, soil depth and crust type affect biocrust microbial communities and networks in Mojave Desert, USA

Biocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Despite there being extensive knowledge on biocrust ecosystem functions and lichen and moss biodiversity, little is known about factors structuring diversity among their microbial communities. We used amplicon-based metabarcode sequencing to survey microbial communities from biocrust surface and subsurface soils at four sites located within the Mojave Desert. Five biocrust types were examined: Light-algal/Cyanobacteria, Cyanolichen, Green-algal lichen, Smooth-moss and Rough-moss crust types. Microbial diversity in biocrusts was structured by several characteristics: (i) central versus southern Mojave sites displayed different community signatures, (ii) indicator taxa of plant-associated fungi (plant pathogens and wood saprotrophs) were identified at each site, (iii) surface and subsurface microbial communities were distinct and (iv) crust types had distinct indicator taxa. Network analysis ranked bacteria-bacteria interactions as the most connected of all within-domain and cross-domain interaction networks in biocrust surface samples. Actinobacteria, Proteobacteria, Cyanobacteria and Ascomycota functioned as hubs among all phyla. The bacteria Pseudonocardia sp. (Pseudonocardiales, Actinobacteria) and fungus Alternaria sp. (Pleosporales, Ascomycota) were the most connected had the highest node degree. Our findings provide crucial insights for dryland microbial community ecology, conservation and sustainable management.

Niche Partitioning with Temperature among Heterocystous Cyanobacteria (Scytonema spp., Nostoc spp., and Tolypothrix spp.) from Biological Soil Crusts

Heterocystous cyanobacteria of biocrusts are key players for biological fixation in drylands, where nitrogen is only second to water as a limiting resource. We studied the niche partitioning among the three most common biocrust heterocystous cyanobacteria sts using enrichment cultivation and the determination of growth responses to temperature in 30 representative isolates. Isolates of Scytonema spp. were most thermotolerant, typically growing up to 40 °C, whereas only those of Tolypothrix spp. grew at 4 °C. Nostoc spp. strains responded well at intermediate temperatures. We could trace the heat sensitivity in Nostoc spp. and Tolypothrix spp. to N₂-fixation itself, because the upper temperature for growth increased under nitrogen replete conditions. This may involve an inability to develop heterocysts (specialized N₂-fixing cells) at high temperatures. We then used a meta-analysis of biocrust molecular surveys spanning four continents to test the relevance of this apparent niche partitioning in nature. Indeed, the geographic distribution of the three types was clearly constrained by the mean local temperature, particularly during the growth season. This allows us to predict a potential shift in dominance in many locales as a result of global warming, to the benefit of Scytonema spp. populations.