A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus

Microbial Sulfur and Arsenic Oxidation Facilitate the Establishment of Biocrusts during Reclamation of Degraded Mine Tailings

Degraded tailings generated by the mining of metal ores are major environmental threats to the surrounding ecosystems. Tailing reclamation, however, is often impeded due to adverse environmental conditions, with depleted key nutrients (i.e., nitrogen (N) and phosphorus (P)) and elevated sulfur and metal(loid) concentrations. Formation of biocrusts may significantly accelerate nutrient accumulation and is therefore an essential stage for tailing reclamation. Although suggested to play an important role, the microbial community composition and key metabolisms in biocrusts remain largely unknown and are therefore investigated in the current study. The results suggested that sulfur and arsenic oxidation are potential energy sources utilized by members of predominant biocrust bacterial families, including Beijerinckiaceae, Burkholderiaceae, Hyphomicrobiaceae, and Rhizobiaceae. Accordingly, the S and As oxidation potentials are elevated in biocrusts compared to those in their adjacent tailings. Biocrust growth, as proxied by chlorophyll concentrations, is enhanced in treatments supplemented with S and As. The elevated biocrust growth might benefit from nutrient acquisition services (i.e., nitrogen fixation and phosphorus solubilization) fueled by microbial sulfur and arsenic oxidation. The current study suggests that sulfur- and arsenic-oxidizing microorganisms may play important ecological roles in promoting biocrust formation and facilitating tailing reclamation.

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.

A direct PCR approach with low-biomass insert opens new horizons for molecular sciences on cryptogam communities

Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method's potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.IMPORTANCECyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.

The global speciation continuum of the cyanobacterium Microcoleus

Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.

Spatial organization of a soil cyanobacterium and its cyanosphere through GABA/Glu signaling to optimize mutualistic nitrogen fixation

Soil biocrusts are characterized by the spatial self-organization of resident microbial populations at small scales. The cyanobacterium Microcoleus vaginatus, a prominent primary producer and pioneer biocrust former, relies on a mutualistic carbon (C) for nitrogen (N) exchange with its heterotrophic cyanosphere microbiome, a mutualism that may be optimized through the ability of the cyanobacterium to aggregate into bundles of trichomes. Testing both environmental populations and representative isolates, we show that the proximity of mutualistic diazotroph populations results in M. vaginatus bundle formation orchestrated through chemophobic and chemokinetic responses to gamma-aminobutyric acid (GABA) /glutamate (Glu) signals. The signaling system is characterized by: a high GABA sensitivity (nM range) and low Glu sensitivity (μM to mM), the fact that GABA and Glu are produced by the cyanobacterium as an autoinduction response to N deficiency, and by the presence of interspecific signaling by heterotrophs in response to C limitation. Further, it crucially switches from a positive to a negative feedback loop with increasing GABA concentration, thus setting maximal bundle sizes. The unprecedented use of GABA/Glu as an intra- and interspecific signal in the spatial organization of microbiomes highlights the pair as truly universal infochemicals.

Cross-Feeding between Filamentous Cyanobacteria and Symbiotic Bacteria Favors Rapid Photogranulation

Photogranules are dense algal-bacterial aggregates used in aeration-free and carbon-negative wastewater treatment, wherein filamentous cyanobacteria (FC) are essential components. However, little is known about the functional role of symbiotic bacteria in photogranulation. Herein, we combined cyanobacterial isolation, reactor operation, and multiomics analysis to investigate the cyanobacterial-bacterial interaction during photogranulation. The addition of FC to the inoculated sludge achieved a 1.4-fold higher granule size than the control, and the aggregation capacity of FC-dominant photogranules was closely related to the extracellular polysaccharide (PS) concentration (R = 0.86). Importantly, we found that cross-feeding between FC and symbiotic bacteria for macromolecular PS synthesis is at the heart of photogranulation and substantially enhanced the granular stability. Chloroflexi-affiliated bacteria intertwined with FC throughout the photogranules and promoted PS biosynthesis using the partial nucleotide sugars produced by FC. Proteobacteria-affiliated bacteria were spatially close to FC, and highly expressed genes for vitamin B1 and B12 synthesis, contributing the necessary cofactors to promote FC proliferation. In addition, Bacteroidetes-affiliated bacteria degraded FC-derived carbohydrates and influenced granules development. Our metabolic characterization identified the functional role of symbiotic bacteria of FC during photogranulation and shed light on the critical cyanobacterial-bacterial interactions in photogranules from the viewpoint of cross-feeding.

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Biocrusts are phototroph-driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth-promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host-microbe co-culture experiments between biocrust communities/biocrust isolates and a model grass (Brachypodium distachyon) or a dominant biocrust cyanobacterium (Microcoleus vaginatus), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates (Bosea sp._L1B56, Pseudarthrobacter sp._L1D14 and Pseudarthrobacter picheli_L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B. distachyon exudates, and supplementation of plant growth medium with this metabolite increased B. distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth-promoting microbes and metabolites.

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.

The β-Lactamase Activity at the Community Level Confers β-Lactam Resistance to Bloom-Forming Microcystis aeruginosa Cells

Many freshwater cyanobacteria, including Microcystis aeruginosa, lack several known antibiotic resistance genes; however, both axenic and xenic M. aeruginosa strains exhibited high antibiotic resistance against many antibiotics under our tested concentrations, including colistin, trimethoprim, and kanamycin. Interestingly, axenic PCC7806, although not the xenic NIBR18 and NIBR452 strains, displayed susceptibility to ampicillin and amoxicillin, indicating that the associated bacteria in the phycosphere could confer such antibiotic resistance to xenic strains. Fluorescence and scanning electron microscopic observations revealed their tight association, leading to possible community-level β-lactamase activity. Combinatory treatment of ampicillin with a β-lactamase inhibitor, sulbactam, abolished the ampicillin resistance in the xenic stains. The nitrocefin-based assay confirmed the presence of significant community-level β-lactamase activity. Our tested low ampicillin concentration and high β-lactamase activity could potentially balance the competitive advantage of these dominant species and provide opportunities for the less competitive species, thereby resulting in higher bacterial diversity under ampicillin treatment conditions. Non-PCR-based metagenome data from xenic NIBR18 cultures revealed the dominance of blaOXA-related antibiotic resistance genes followed by other class A β-lactamase genes (AST-1 and FAR-1). Alleviation of ampicillin toxicity could be observed only in axenic PCC7806, which had been cocultured with β-lactamase from other freshwater bacteria. Our study suggested M. aeruginosa develops resistance to old-class β-lactam antibiotics through altruism, where associated bacteria protect axenic M. aeruginosa cells.

The phyto-bacterioplankton couple in a shallow freshwater ecosystem: Who leads the dance?

Bloom-forming phytoplankton dynamics are still unpredictable, even though it is known that several abiotic factors, such as nutrient availability and temperature, are key factors for bloom development. We investigated whether biotic factors, i.e. the bacterioplankton composition (via 16SrDNA metabarcoding), were correlated with phytoplankton dynamics, through a weekly monitoring of a shallow lake known to host recurrent cyanobacterial blooms. We detected concomitant changes in both bacterial and phytoplankton community biomass and diversity. During the bloom event, a significant decrease in phytoplankton diversity, was detected, with a first co-dominance of Ceratium, Microcystis and Aphanizomenon, followed by a co-dominance of the two cyanobacterial genera. In the same time, we observed a decrease of the particle-associated (PA) bacterial richness and the emergence of a specific bacterial consortium that was potentially better adapted to the new nutritional niche. Unexpectedly, changes in PA bacterial communities occurred just before the development the emergence of the phytoplanktonic bloom and the associated modification of the phytoplanktonic community composition, suggesting that changes in environmental conditions leading to the bloom, were first sensed by the bacterial PA community. This last was quite stable throughout the bloom event, even though there were changes in the blooming species, suggesting that the association between cyanobacterial species and bacterial communities may not be as tight as previously described for monospecific blooming communities. Finally, the dynamics of the free-living (FL) bacterial communities displayed a different trajectory from those of the PA and phytoplankton communities. This FL communities can be viewed as a reservoir for bacterial recruitment for the PA fraction. Altogether, these data also highlight s that the spatial organization within these different microenvironments in the water column is a relevant factor in the structuring of these communities.

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.

Impact of dehydration on the physiochemical properties of Nostoc calcicola BOT1 and its untargeted metabolic profiling through UHPLC-HRMS

The global population growth has led to a higher demand for food production, necessitating improvements in agricultural productivity. However, abiotic and biotic stresses pose significant challenges, reducing crop yields and impacting economic and social welfare. Drought, in particular, severely constrains agriculture, resulting in unproductive soil, reduced farmland, and jeopardized food security. Recently, the role of cyanobacteria from soil biocrusts in rehabilitating degraded land has gained attention due to their ability to enhance soil fertility and prevent erosion. The present study focused on Nostoc calcicola BOT1, an aquatic, diazotrophic cyanobacterial strain collected from an agricultural field at Banaras Hindu University, Varanasi, India. The aim was to investigate the effects of different dehydration treatments, specifically air drying (AD) and desiccator drying (DD) at various time intervals, on the physicochemical properties of N. calcicola BOT1. The impact of dehydration was assessed by analyzing the photosynthetic efficiency, pigments, biomolecules (carbohydrates, lipids, proteins, osmoprotectants), stress biomarkers, and non-enzymatic antioxidants. Furthermore, an analysis of the metabolic profiles of 96-hour DD and control mats was conducted using UHPLC-HRMS. Notably, there was a significant decrease in amino acid levels, while phenolic content, fatty acids, and lipids increased. These changes in metabolic activity during dehydration highlighted the presence of metabolite pools that contribute to the physiological and biochemical adjustments of N. calcicola BOT1, mitigating the impact of dehydration to some extent. Overall, present study demonstrated the accumulation of biochemical and non-enzymatic antioxidants in dehydrated mats, which could be utilized to stabilize unfavorable environmental conditions. Additionally, the strain N. calcicola BOT1 holds promise as a biofertilizer for semi-arid regions.

Novel biological aqua crust enhances in situ metal(loid) bioremediation driven by phototrophic/diazotrophic biofilm

BACKGROUND

Understanding the ecological and environmental functions of phototrophic biofilms in the biological crust is crucial for improving metal(loid) (e.g. Cd, As) bioremediation in mining ecosystems. In this study, in combination with metal(loid) monitoring and metagenomic analysis, we systematically evaluated the effect of biofilm in a novel biological aqua crust (biogenic aqua crust-BAC) on in situ metal(loid) bioremediation of a representative Pb/Zn tailing pond.

RESULTS

We observed strong accumulation of potentially bioavailable metal(loid)s and visible phototrophic biofilms in the BAC. Furthermore, dominating taxa Leptolyngbyaceae (10.2-10.4%, Cyanobacteria) and Cytophagales (12.3-22.1%, Bacteroidota) were enriched in biofilm. Along with predominant heterotrophs (e.g. Cytophagales sp.) as well as diazotrophs (e.g. Hyphomonadaceae sp.), autotrophs/diazotrophs (e.g. Leptolyngbyaceae sp.) in phototrophic biofilm enriched the genes encoding extracellular peptidase (e.g. family S9, S1), CAZymes (e.g. CBM50, GT2) and biofilm formation (e.g. OmpR, CRP and LuxS), thus enhancing the capacity of nutrient accumulation and metal(loid) bioremediation in BAC system.

CONCLUSIONS

Our study demonstrated that a phototrophic/diazotrophic biofilm constitutes the structured communities containing specific autotrophs (e.g. Leptolyngbyaceae sp.) and heterotrophs (e.g. Cytophagales sp.), which effectively control metal(loid) and nutrient input using solar energy in aquatic environments. Elucidation of the mechanisms of biofilm formation coupled with metal(loid) immobilization in BAC expands the fundamental understanding of the geochemical fate of metal(loid)s, which may be harnessed to enhance in situ metal(loid) bioremediation in the aquatic ecosystem of the mining area. Video Abstract.

The interplay between microalgae and toxic metal(loid)s: mechanisms and implications in AMD phycoremediation coupled with Fe/Mn mineralization

Acid mine drainage (AMD) is low-pH with high concentration of sulfates and toxic metal(loid)s (e.g. As, Cd, Pb, Cu, Zn), thereby posing a global environmental problem. For decades, microalgae have been used to remediate metal(loid)s in AMD, as they have various adaptive mechanisms for tolerating extreme environmental stress. Their main phycoremediation mechanisms are biosorption, bioaccumulation, coupling with sulfate-reducing bacteria, alkalization, biotransformation, and Fe/Mn mineral formation. This review summarizes how microalgae cope with metal(loid) stress and their specific mechanisms of phycoremediation in AMD. Based on the universal physiological characteristics of microalgae and the properties of their secretions, several Fe/Mn mineralization mechanisms induced by photosynthesis, free radicals, microalgal-bacterial reciprocity, and algal organic matter are proposed. Notably, microalgae can also reduce Fe(III) and inhibit mineralization, which is environmentally unfavorable. Therefore, the comprehensive environmental effects of microalgal co-occurring and cyclical opposing processes must be carefully considered. Using chemical and biological perspectives, this review innovatively proposes several specific processes and mechanisms of Fe/Mn mineralization that are mediated by microalgae, providing a theoretical basis for the geochemistry of metal(loid)s and natural attenuation of pollutants in AMD.

Metagenome-Based Exploration of Bacterial Communities Associated with Cyanobacteria Strains Isolated from Thermal Muds

Cyanobacteria constitute a pioneer colonizer of specific environments for whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through the exchange and recycling of key nutrients and the sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated, along with their associated cyanospheres, from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among the members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic descriptions of the microbial consortia. The results provided insights into the potential role and metabolic capabilities of the microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity, and genetic potential functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlighted the great influence of the reference protein database chosen for performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately covers both autotroph and heterotroph metabolic specificities.

Metabolites Facilitating Adaptation of Desert Cyanobacteria to Extremely Arid Environments

Desert is one of the harshest environments on the planet, characterized by exposure to daily fluctuations of extreme conditions (such as high temperature, low nitrogen, low water, high salt, etc.). However, some cyanobacteria are able to live and flourish in such conditions, form communities, and facilitate survival of other organisms. Therefore, to ensure survival, desert cyanobacteria must develop sophisticated and comprehensive adaptation strategies to enhance their tolerance to multiple simultaneous stresses. In this review, we discuss the metabolic pathways used by desert cyanobacteria to adapt to extreme arid conditions. In particular, we focus on the extracellular polysaccharides and compatible solutes biosynthesis pathways and their evolution and special features. We also discuss the role of desert cyanobacteria in the improvement of soil properties and their ecological and environmental impact on soil communities. Finally, we summarize recent achievements in the application of desert cyanobacteria to prevent soil erosion and desertification.

Towards large scale biocrust restoration: Producing an efficient and low-cost inoculum of N-fixing cyanobacteria

Dryland soil degradation is increasing due to global change and traditional restoration methods are not successful due to water scarcity. Thus, an alternative technology based on inoculating biocrust-forming cyanobacteria on degraded soils has emerged. Biocrusts are communities of mosses, lichens, cyanobacteria or fungi that colonize soil surface forming a stable and fertile layer. Previous studies have shown the benefits of inoculating cyanobacteria to restore soils at a small scale. However, to face field restoration projects, it is necessary to produce high quantities of biomass at an affordable cost. In this work, we analyze if the previously tested cyanobacteria Scytonema hyalinum, Tolypothrix distorta (heterocystous strains) and Trichocoleus desertorum (a bundle-forming one) can be produced with agricultural fertilizers. Different culture media were used: two containing pure chemicals (BG11 and BG11₀, this N-free medium was used just for heterocystous strains) and two containing fertilizers (BG11-F and MM-F). The performance of the cultures was monitored by measuring the biomass concentration and photosynthetic stress. Afterwards, we analyzed their capacity to induce biocrusts and improve soil properties by inoculating the biomass on a mine substrate indoors and measuring, three months later, the albedo, chlorophyll a and organic carbon content. Results show that the bundle-forming cyanobacterium was unable to grow in the media tested, whereas both heterocystous cyanobacteria grew in all of them and induced the formation of biocrusts improving the organic carbon substrate content. The best results for S. hyalinum were found using the MM-F medium, and for T. distorta using a medium containing pure chemicals (BG11). However, results were also positive when using a medium containing fertilizers (BG11-F). Thus, agricultural fertilizers can be used to undertake the production of heterocystous cyanobacteria for large scale restoration in drylands. On the other hand, more research is needed to find sustainable techniques to produce biomass of bundle-forming cyanobacteria.

Spatial self-segregation of pioneer cyanobacterial species drives microbiome organization in biocrusts

Microbial communities are typically characterized by some degree of self-organization. In biological soil crust (biocrust) communities, vertical organization of resident populations at the mm scale is driven by organismal adaptations to physicochemical microniches. However, the extent of horizontal organization and its driving processes are unknown. Using a combination of observational and genetic mapping, we provide evidence for a highly defined, horizontal self-organization (patchiness) at the mm to cm scale in a successionally early biocrust community dominated by the pioneer cyanobacteria, Microcoleus vaginatus (Microcoleaceae) and Parifilum sp. (Coleofasciculaceae). Experiments with representative isolates of each species demonstrate that the phenomenon is driven by active spatial segregation based on cross-species sensing through the exometabolome acted upon with motility responses. Further, we show that both species share the ability to enrich for specialized cyanospheres of heterotrophic bacteria at smaller scales, and that these cyanospheres are characterized by compositional host-specificity, thus expanding the reach of spatial patchiness beyond primary producers. Our results highlight the importance of specific microbial interactions in the emergence of microbiome compositional architecture and the enhancement of microbial diversity.

Rainfall pulse regime drives biomass and community composition in biological soil crusts

Future climates will alter the frequency and size of rain events in drylands, potentially affecting soil microbes that generate carbon feedbacks to climate, but field tests are rare. Topsoils in drylands are commonly colonized by biological soil crusts (biocrusts), photosynthesis-based communities that provide services ranging from soil fertilization to stabilization against erosion. We quantified responses of biocrust microbial communities to twelve years of altered rainfall regimes, with 60 mm of additional rain per year delivered either as small (5 mm) weekly rains or large (20 mm) monthly rains during the summer monsoon season. Rain addition promoted microbial diversity, suppressed the dominant cyanobacterium, Microcoleus vaginatus, and enhanced nitrogen-fixing taxa, but did not consistently increase microbial biomass. The addition of many small rain events increased microbial biomass, whereas few, large events did not. These results alter the physiological paradigm that biocrusts are most limited by the amount of rainfall and instead predict that regimes enriched in small rain events will boost cyanobacterial biocrusts and enhance their beneficial services to drylands. This article is protected by copyright. All rights reserved.

Physical Disturbance Reduces Cyanobacterial Relative Abundance and Substrate Metabolism Potential of Biological Soil Crusts on a Gold Mine Tailing of Central China

As the critical ecological engineers, biological soil crusts (biocrusts) are considered to play essential roles in improving substrate conditions during ecological rehabilitation processes. Physical disturbance, however, often leads to the degradation of biocrusts, and it remains unclear how the physical disturbance affects biocrust microorganisms and their related metabolism. In this study, the photosynthetic biomass (indicated by chlorophyll a), nutrients, enzyme activities, and bacterial communities of biocrusts were investigated in a gold mine tailing of Central China to evaluate the impact of physical disturbance on biocrusts during the rehabilitation process of gold mine tailings. The results show that physical disturbance significantly reduced the photosynthetic biomass, nutrient contents (organic carbon, ammonium nitrogen, nitrate nitrogen, and total phosphorus), and enzyme activities (β-glucosidase, sucrase, nitrogenase, neutral phosphatase, and urease) of biocrusts in the mine tailings. Furthermore, 16S rDNA sequencing showed that physical disturbance strongly changed the composition, structure, and interactions of the bacterial community, leading to a shift from a cyanobacteria dominated community to a heterotrophic bacteria (proteobacteria, actinobacteria, and acidobacteria) dominated community and a more complex bacterial network (higher complexity, nodes, and edges). Altogether, our results show that the biocrusts dominated by cyanobacteria could also develop in the tailings of humid region, and the dominants (e.g., Microcoleus) were the same as those from dryland biocrusts; nevertheless, physical disturbance significantly reduced cyanobacterial relative abundance in biocrusts. Based on our findings, we propose the future work on cyanobacterial inoculation (e.g., Microcoleus), which is expected to promote substrate metabolism and accumulation, ultimately accelerating the development of biocrusts and the subsequent ecological restoration of tailings.

Responses of the Soil Bacterial Community, Resistome, and Mobilome to a Decade of Annual Exposure to Macrolide Antibiotics

Biosolids that are applied to agricultural soil as an organic fertilizer are frequently contaminated with pharmaceutical residues that have persisted during wastewater treatment and partitioned into the organic phase. Macrolide antibiotics, which serve as a critically important human medicine, have been detected within biosolids. To determine the impacts of macrolide antibiotics on soil bacteria, every year for a decade, a series of replicated field plots received an application of a mixture of erythromycin, clarithromycin, and azithromycin at a realistic (0.1 mg kg soil^-1) or an unrealistically high (10 mg kg soil^-1) dose or were left untreated. The effects of repeated antibiotic exposure on the soil bacterial community, resistome, mobilome, and integron gene cassette content were evaluated by 16S rRNA and integron gene cassette amplicon sequencing, as well as whole-metagenome sequencing. At the unrealistically high dose, the overall diversity of the resistome and mobilome was altered, as 21 clinically important antibiotic resistance genes predicted to encode resistance to 10 different antibiotic drug classes were increased and 20 mobile genetic element variants (tnpA, intI1, tnpAN, and IS91) were increased. In contrast, at the realistic dose, no effect was observed on the overall diversity of the soil bacterial community, resistome, mobilome, or integron gene cassette-carrying genes. Overall, these results suggest that macrolide antibiotics entrained into soil at concentrations anticipated with biosolid applications would not result in major changes to these endpoints. IMPORTANCE Biosolids, produced from the treatment of sewage sludge, are rich in plant nutrients and are a valuable alternative to inorganic fertilizer when applied to agricultural soil. However, the use of biosolids in agriculture, which are frequently contaminated with pharmaceuticals, such as macrolide antibiotics, may pose a risk to human health by selecting for antibiotic resistance genes that could be transferred to plant-based food destined for human consumption. The consequences of long-term, repeated macrolide antibiotic exposure on the diversity of the soil bacterial community, resistome, and mobilome were evaluated. At unrealistically high concentrations, macrolide antibiotics alter the overall diversity of the resistome and mobilome, enriching for antibiotic resistance genes and mobile genetic elements of concern to human health. However, at realistic antibiotic concentrations, no effect on these endpoints was observed, suggesting that current biosolids land management practices are unlikely to pose a risk to human health due to macrolide antibiotic contamination alone.

Cyanobacterial community composition and their functional shifts associated with biocrust succession in the Gurbantunggut Desert

Cyanobacteria, as key biocrust components, provide a variety of ecosystem functions in drylands. In this study, to identify whether a cyanobacterial community shift is involved in biocrust succession and whether this is linked to altered ecological functions, we investigated cyanobacterial composition, total carbon and nitrogen contents of biocrusts in the Gurbantunggut Desert. Our findings showed that the biocrust cyanobacteria in the Gurbantunggut desert were mostly filamentous, coexisting with abundant unicellular colonial Chroococcidiopsis. Heterocystous Nostoc, Scytonema and Tolypothrix always represented the majority of biocrust nitrogen-fixing organisms, comprising an average of 92% of the nifH gene reads. Community analysis showed a clear shift in prokaryotic community composition associated with biocrust succession from cyanobacteria- to lichen- and moss-dominated biocrusts, and filamentous non-nitrogen-fixing cyanobacteria-dominated communities were gradually replaced by nitrogen-fixing and unicellular colonial communities. Along the succession, there were concomitant reductions in cyanobacterial relative abundance, whereas Chl-a, total carbon and nitrogen contents increased. Concurrently, distinct carbon and nitrogen stores shifts occurred, implying that the main ecological contribution of cyanobacteria in biocrusts changes from carbon- to nitrogen-fixation along with the succession. Our results suggest that any activity that reverses biocrust succession will influence cyanobacterial community composition and eventually lead to large reductions in soil carbon and nitrogen stores.

Cyanobacterial persistence and influence on microbial community dynamics over 15 years in induced biocrusts

Biocrusts provide numerous ecological functions in drylands. Recovering biocrusts via cyanobacterial inoculation recently gathered interest for ecological restoration, yet it still lacks long-term experiments to unravel biocrust community dynamics. To examine how cyanobacterial inoculants influenced local microbial community and biocrust development, we observed a 2 km² (Qubqi Desert, China) inoculation experiment after 10 and 15 years, following biocrust formation. Our results revealed that biocrust development was in line with ecological regime shift, providing evidence for biocrust community succession, from cyanobacteria- to moss-dominated types. Associated with biocrust development, microbial communities differed significantly with less specialists compared to shifting sands. Cyanobacterial community analysis showed that Microcoleus vaginatus and Scytonema javanicum are an ideal inoculating model, as they were still dominating the community after 15 years since inoculation, while other nitrogen-fixing cyanobacteria occurred profusely with biocrust development. Biocrust community composition combined with thickness, Chl-a and exopolysaccharide measurements revealed the large variation of cyanobacterial ecological functions along biocrust development, suggesting a main function shift: from carbon fixation associated with exopolysaccharide secretion in bare sandy soils to nitrogen fixation in developed biocrusts. This large-scale field study verifies that cyanobacterial inoculation accelerates biocrust development and forwards succession, shaping the biocrust community composition over a long time.

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.

Role of Bacillus inoculation in rice straw composting and bacterial community stability after inoculation: Unite resistance or individual collapse

Bacillus is the classic inoculant in rice straw composting. However, there has been no in-depth study of the mechanism promoting the degradation of lignocellulose and the change of indigenous bacterial communities after Bacillus inoculation. Moreover, the stability of bacterial communities is a significant challenge in achieving the efficacy of inoculation. In this study, the ecological succession and yield-resource acquisition-stress tolerance (Y-A-S) framework were combined with Redundancy analysis (RDA) and changes in relative abundance, Bacillus was found to be a pioneer bacterium that adopts a resource acquisition-stress tolerance strategy. The structural equation model (SEM) revealed that in addition to exerting a degradation effect, Bacillus inoculation could also indirectly affect lignocellulose degradation by changing the bacterial community. Random forest model and network analysis indicated a change in bacterial communities after inoculation, and bacteria with more complex relationships and weaker decomposition ability were key to the stability of bacterial communities.

Beneficial cyanosphere heterotrophs accelerate establishment of cyanobacterial biocrust

Biological soil crusts (biocrusts) are communities of microbes that inhabit the surface of arid soils and provide essential services to dryland ecosystems. While resistant to extreme environmental conditions, biocrusts are susceptible to anthropogenic disturbances that can deprive ecosystems of these valuable services for decades. Until recently, culture-based efforts to produce inoculum for cyanobacterial biocrust restoration in the Southwestern US focused on producing and inoculating the most abundant primary producers and biocrust pioneers, Microcoleus vaginatus and members of the family Coleofasciculaceae (aka "Microcoleus streenstrupii complex"). The discovery that a unique microbial community characterized by diazotrophs is intimately associated with M. vaginatus, known as the "cyanosphere", suggests a symbiotic division of labor in which nutrients are traded between phototrophs and heterotrophs. To probe the potential use of such cyanosphere members in the restoration of biocrusts, we performed co-inoculations of soil substrates with cyanosphere constituents. This resulted in more rapid cyanobacterial growth over inoculations with the cyanobacterium alone. Additionally, we found that the mere addition of beneficial heterotrophs enhanced the formation of a cohesive biocrust without the need of additional phototrophic biomass within native soils that contain trace amounts of biocrust cyanobacteria. Our findings support the hitherto unknown role of beneficial heterotrophic bacteria in the establishment and growth of biocrusts and allow us to make recommendations concerning biocrust restoration efforts based on the presence of remnant biocrust communities in disturbed areas. Future biocrust restoration efforts should consider cyanobacteria and their beneficial heterotrophic community as inoculants. Importance The advancement of biocrust restoration methodologies for cyanobacterial biocrusts has been largely achieved through trial and error. Successes and failures could not always be traced back to particular factors. The investigation and application of foundational microbial interactions existing within biocrust communities is a crucial step toward informed and repeatable biocrust restoration methodologies.

Reading and surviving the harsh conditions in desert biological soil crust: The cyanobacterial viewpoint

Biological soil crusts (BSCs) are found in drylands, cover ∼12% of the Earth's surface in arid and semi-arid lands and their destruction is considered an important promoter of desertification. These crusts are formed by the adhesion of soil particles to polysaccharides excreted mostly by filamentous cyanobacteria, which are the pioneers and main primary producers in BSCs. Desert BSCs survive in one of the harshest environments on Earth, and are exposed to daily fluctuations of extreme conditions. The cyanobacteria inhabiting these habitats must precisely read the changing conditions and predict, for example, the forthcoming desiccation. Moreover, they evolved a comprehensive regulation of multiple adaptation strategies to enhance their stress tolerance. Here we focus on what distinguishes cyanobacteria able to revive after dehydration from those that cannot. While important progress has been made in our understanding of physiological, biochemical and omics aspects, clarification of the sensing, signal transduction and responses enabling desiccation tolerance are just emerging. We plot the trajectory of current research and open questions ranging from general strategies and regulatory adaptations in the hydration/desiccation cycle, to recent advances in our understanding of photosynthetic adaptation. The acquired knowledge provides new insights to mitigate desertification and improve plant productivity under drought conditions.

Algae Biofilm Reduces Microbe-Derived Dissolved Organic Nitrogen Discharges: Performance and Mechanisms

Microbe-derived dissolved organic nitrogen (mDON) can readily induce harmful phytoplankton blooms, and thus, restricting its discharges is necessary. Recently, algae biofilm (AB) has attracted increasing interest for its advantages in nutrient recovery. However, its features in mDON control remain unexplored. Herein, AB's mDON formation and utilization performance, molecular characteristics, and metabolic traits have been investigated, with activated sludge (AS) as the benchmark for comparisons. Comparatively, AB reduced mDON formation by 83% when fed with DON-free wastewater. When fed with AS's effluent, it consumed at least 72% of the exogenous mDON and notably reduced the amount of protein/amino sugar-like compounds. Irrespective of the influent, AB ultimately produced more various unsaturated hydrocarbon and lignin analogues. Redundancy and network analysis highlighted the algal-bacterial synergistic effects exemplified by cross-feeding in reducing mDON concentrations and shaping mDON pools. Moreover, metagenomics-based metabolic reconstruction revealed that cyanobacteria Limnothrix and Kamptonema spp. facilitated mDON uptake, ammonification, and recycling, which supplied the extensive nitrogen assimilatory demand for amino acids, vitamins, and cofactors biosynthesis, and therefore promoted mDON scavenging. Our findings demonstrate that regardless of the secondary or tertiary process, cyanobacteria-dominated AB is promising to minimize bioavailable mDON discharges, which has implications for future eutrophication control.