A natural view of microbial biodiversity within hot spring cyanobacterial mat communities

Energetic investigations of Acidianus ambivalens metabolism during anaerobic sulfur reduction and comparisons to aerobic sulfur oxidation

Acidianus ambivalens is a metabolically flexible facultative anaerobe that can oxidize and reduce elemental sulfur with O2 and H2, respectively. In this work, the growth energetics of Acidianus ambivalens were determined under anaerobic conditions at 76 °C with H2 oxidation by elemental sulfur serving as the energy-yielding catabolic reaction. The biomass yields (C-mol of biomass per mol of H2 consumed) ranged from approximately 0.004 to 0.01. Growth rates ranged from 0.003 to 0.012 h-1. Gibbs energies of incubation based on macrochemical equations of cell growth ranged from - 881 to - 3349 kJ/C-mol. Enthalpies of incubation determined from calorimetric measurements ranged from - 610 to - 4090 kJ/C-mol. The Gibbs energy consumed by anaerobic cultures was compared to sulfur-oxidizing cultures under aerobic and microaerobic conditions to determine the effects of environmental and substrate redox state on energetics. This comparison revealed that aerobic cultures were inefficient relative to microaerobic and anaerobic conditions. These results suggest that aerobic conditions induce a measurable oxidative stress on cultures. The similarities in growth efficiency and energy budgets under microaerobic and anaerobic conditions may allow Acidianus ambivalens to be competitive in natural environments either by oxidizing or reducing elemental sulfur.

Abundant and active community members respond to diel cycles in hot spring phototrophic mats

Photosynthetic microbial mats in hot springs can provide insights into the diel behaviors of communities in extreme environments. In this habitat, photosynthesis dominates during the day, leading to super-oxic conditions, with a rapid transition to fermentation and anoxia at night. Multiple samples were collected from two springs over several years to generate metagenomic and metatranscriptomic datasets. Metagenome-assembled genomes comprised 71 taxa (in 19 different phyla), of which 12 core taxa were present at high abundance in both springs. The eight most active taxa identified by metatranscriptomics were an oxygenic cyanobacterium (Synechococcus sp.), five anoxygenic phototrophs from three different phyla, and two understudied heterotrophs from phylum Armatimonadota. In all eight taxa, a significant fraction of genes exhibited a diel expression pattern, although peak timing varied considerably. The two abundant heterotrophs exhibit starkly different peak timing of expression, which we propose is shaped by their metabolic and genomic potential to use carbon sources that become differentially available during the diel cycle. Network analysis revealed pathway expression patterns that had not previously been linked to diel cycles, including ribosome biogenesis and chaperones. This provides a framework for analyzing metabolically coupled communities and the dominant role of the diel cycle.

Diversity and networking of uni-cyanobacterial cultures and associated heterotrophic bacteria from the benthic microbial mat of a desert hydrothermal spring

Thermal springs harbour microorganisms, often dominated by cyanobacteria, which form biofilms and microbial mats. These phototrophic organisms release organic exudates into their immediate surroundings, attracting heterotrophic bacteria that contribute to the diversity and functioning of these ecosystems. In this study, the microbial mats from a hydrothermal pool in the Ksar Ghilane oasis in the Grand Erg Oriental of the Desert Tunisia were collected to obtain cyanobacterial cultures formed by single cyanobacterial species. High-throughput analysis showed that while the microbial mat hosted diverse cyanobacteria, laboratory cultures selectively enriched cyanobacteria from the Leptolyngbya, Nodosilinea, and Arthronema. Per each of these genera, multiple non-axenic uni-cyanobacterial cultures were established, totalling 41 cultures. Cyanobacteria taxa mediated the assembly of distinct heterotrophic bacterial communities, with members of the Proteobacteria and Actinobacteria phyla dominating. The bacterial communities of uni-cyanobacterial cultures were densely interconnected, with heterotrophic bacteria preferentially co-occurring with each other. Our study highlighted the complex structures of non-axenic uni-cyanobacterial cultures, where taxonomically distinct cyanobacteria consistently associate with specific groups of heterotrophic bacteria. The observed associations were likely driven by common selection pressures in the laboratory, such as cultivation conditions and specific hosts, and may not necessarily reflect the microbial dynamic occurring in the spring microbial mats.

Microbial and mineralogical characterization of the alkaline Chae Son hot spring, Northern Thailand

Early characterizations by morphological identification through light microscopy only revealed the presence of a few microbial lineages and the majority of microbial community at the Chae Son hot spring remains uncharacterized. Therefore, this study aims to examine thermophilic microbial communities at the Chae Son hot spring using next-generation sequencing, including investigating hot spring mineralogy. Results suggest that the Chae Son hot spring (49-75 °C, pH = 6.5-7.0) precipitates digitate structures which comprise mainly silica, and that microbial permineralization is primarily through silicification. Alternating layers of mineralized microbial biofilms and silica were observed in digitate sinter cross-sections, contributing to the build-up of microstromatolites. Molecular results revealed that phylogenetically distinct members of photoautotrophic taxa, Chloroflexota and Cyanobacteriota, dominated spring microbial communities (63.19% relative abundance). Potential primary production processes were mainly through photoautotrophy, with minor lithoautotrophic activities (e.g., sulfur cycling and nitrogen cycling). Moreover, overall microbial community and Cyanobacteriota population alpha diversities significantly decreased with increased temperatures. However, no significant correlation was identified between Chloroflexota population diversity and temperatures. This study provides an update on the microbial community using a high-throughput next-generation sequencing technology, including the mineralogy of the Chae Son hot spring, Northern Thailand.

Modern microbiology: Embracing complexity through integration across scales

Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.

Molecular diversity of green-colored microbial mats from hot springs of northern Japan

We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.

Mineralogical and microbial characterization of alkali hot spring microbial mats and deposits in Pong Dueat Pa Pae hot spring, Northern Thailand

Hot spring environments encompass broad physicochemical ranges, in which temperature and pH account for crucial factors shaping hot spring microbial community and diversity. However, the presence of photosynthetic microbial mats adjacent to boiling hot spring vents, where fluid temperatures extend beyond photosynthetic capability, questions the microbial profiles and the actual temperatures of such adjacent mats. Therefore, this study aims to characterize thermophilic microbial communities at Pong Dueat Pa Pae hot spring using next-generation sequencing, including investigating hot spring mineralogy. Results suggest that Pong Dueat Pa Pae hot spring precipitates comprise mainly silica which also acts as the main preservative medium for microbial permineralization. Molecular results revealed the presence of cyanobacterial and Chloroflexi species in the thick, orange and green subaerial mats surrounding the vents, suggesting the mats would be at least 30 °C cooler than source vents despite constantly receiving geyser splashes. Bacterial abundance was considerably higher than archaeal (97.9% versus 2.1%). Cyanobacterial (mainly Synechococcus and Leptolygbya) and Chloroflexi species (mainly Roseiflexus) accounted for almost half (40.04%) of the bacterial community, while DHVEG-6 and Thaumarchaeota comprised dominant members (> 90%) of the archaeal fraction. This study updates and provides insights into thermophilic microbial community composition and mineralogy of hot springs in Thailand.

An improved protocol for metagenomic DNA isolation from low microbial biomass alkaline hot-spring sediments and soil samples

High-quality, humic-acid-free pure DNA is a prerequisite for functional and sequence-based approaches of metagenomics. In the present investigation, an improved extraction buffer was developed by making a combination of powdered activated charcoal (2%; w/v), polyvinyl poly pyrrolidone (2%; w/v), and CaCl2 (2%; w/v). This trio significantly improved the purity and yield of the metagenomic DNA from the hot spring's hot and alkaline soil. The quality of extracted metagenomic DNA was successfully validated by PCR amplification and restriction enzymes. Besides, the thermophilic amylase encoding genes were also retrieved from these soil DNA samples. Extreme habitats I harbour low microbial biomass and, therefore, demand in-situ lysis of the microbial cells to access their genomes. The protocol can potentially extract DNA from geothermal spring habitats where the count of microbial cells is low.

Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities

Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.

An Overview of Lipid Biomarkers in Terrestrial Extreme Environments with Relevance for Mars Exploration

Lipid molecules are organic compounds, insoluble in water, and based on carbon-carbon chains that form an integral part of biological cell membranes. As such, lipids are ubiquitous in life on Earth, which is why they are considered useful biomarkers for life detection in terrestrial environments. These molecules display effective membrane-forming properties even under geochemically hostile conditions that challenge most of microbial life, which grants lipids a universal biomarker character suitable for life detection beyond Earth, where a putative biological membrane would also be required. What discriminates lipids from nucleic acids or proteins is their capacity to retain diagnostic information about their biological source in their recalcitrant hydrocarbon skeletons for thousands of millions of years, which is indispensable in the field of astrobiology given the time span that the geological ages of planetary bodies encompass. This work gathers studies that have employed lipid biomarker approaches for paleoenvironmental surveys and life detection purposes in terrestrial environments with extreme conditions: hydrothermal, hyperarid, hypersaline, and highly acidic, among others; all of which are analogous to current or past conditions on Mars. Although some of the compounds discussed in this review may be abiotically synthesized, we focus on those with a biological origin, namely lipid biomarkers. Therefore, along with appropriate complementary techniques such as bulk and compound-specific stable carbon isotope analysis, this work recapitulates and reevaluates the potential of lipid biomarkers as an additional, powerful tool to interrogate whether there is life on Mars, or if there ever was.

Microbial Diversity and Authigenic Mineral Formation of Modern Bottom Sediments in the Littoral Zone of Lake Issyk-Kul, Kyrgyz Republic (Central Asia)

This article presents geochemical, mineralogical and microbiological characteristics of five samples of modern bottom sediments in the littoral zone of the high-mountain salty lake Issyk-Kul. The 16S rRNA gene sequencing method shows that the microbial community consists of organic carbon degraders (representatives of phyla: Proteobacteria, Chloroflexi, Bacteroidota and Verrucomicrobiota and families Anaerolineaceae and Hungateiclostridiaceae), photosynthetic microorganisms (representatives of Chloroflexi, phototrophic Acidobacteria, purple sulphur bacteria Chromatiaceae and cyanobacteria) and bacteria of the reducing branches of the sulphur biogeochemical cycle (representatives of Desulfobacterota, Desulfosarcinaceae and Desulfocapsaceae). The participation of microorganisms in processes in the formation of a number of authigenic minerals (calcite, framboidal pyrite, barite and amorphous Si) is established. The high diversity of microbial communities indicates the presence of labile organic components involved in modern biogeochemical processes in sediments. The active destruction of organic matter begins at the water-sediment interface.

Factors influencing carrion communities are only partially consistent with those of deadwood necromass

Research on decomposer communities has traditionally focused on plant litter or deadwood. Even though carrion forms highly nutrient-rich necromass that enhance ecosystem heterogeneity, the factors influencing saprophytic communities remain largely unknown. For deadwood, experiments have shown that different drivers determine beetles (i.e., decay stage, microclimate, and space), fungi (i.e., decay stage and tree species) and bacteria (decay stage only) assemblages. To test the hypothesis that similar factors also structure carrion communities, we sampled 29 carcasses exposed for 30 days that included Cervus elaphus (N = 6), Capreolus capreolus (N = 18), and Vulpes vulpes (N = 5) in a mountain forest throughout decomposition. Beetles were collected with pitfall traps, while microbial communities were characterized using amplicon sequencing. Assemblages were determined with a focus from rare to dominant species using Hill numbers. With increasing focus on dominant species, the relative importance of carcass identity on beetles and space on bacteria increased, while only succession and microclimate remained relevant for fungi. For beetle and bacteria with focus on dominant species, host identity was more important than microclimate, which is in marked contrast to deadwood. We conclude that factors influencing carrion saprophytic assemblages show some consistency, but also differences from those of deadwood assemblages, suggesting that short-lived carrion and long-lasting deadwood both provide a resource pulse with different adaptions in insects and microbes. As with deadwood, a high diversity of carcass species under multiple decay stages and different microclimates support a diverse decomposer community.

Is biofilm formation intrinsic to the origin of life?

Biofilms are multicellular, often surface-associated, communities of autonomous cells. Their formation is the natural mode of growth of up to 80% of microorganisms living on this planet. Biofilms refractory towards antimicrobial agents and the actions of the immune system due to their tolerance against multiple environmental stresses. But how did biofilm formation arise? Here, I argue that the biofilm lifestyle has its foundation already in the fundamental, surface-triggered chemical reactions and energy preserving mechanisms that enabled the development of life on earth. Subsequently, prototypical biofilm formation has evolved and diversified concomitantly in composition, cell morphology and regulation with the expansion of prokaryotic organisms and their radiation by occupation of diverse ecological niches. This ancient origin of biofilm formation thus mirrors the harnessing environmental conditions that have been the rule rather than the exception in microbial life. The subsequent emergence of the association of microbes, including recent human pathogens, with higher organisms can be considered as the entry into a nutritional and largely stress-protecting heaven. Nevertheless, basic mechanisms of biofilm formation have surprisingly been conserved and refunctionalized to promote sustained survival in new environments.

HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method

HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. HGTree was constructed in 2015, and a large number of prokaryotic genomes have been additionally published since then. To cope with the rapid rise of prokaryotic genome data, we present HGTree v2.0 (http://hgtree2.snu.ac.kr), a newly updated version of our HGT database with much more extensive data, including a total of 20 536 completely sequenced non-redundant prokaryotic genomes, and more reliable HGT information results curated with various steps. As a result, HGTree v2.0 has a set of expanded data results of 6 361 199 putative horizontally transferred genes integrated with additional functional information such as the KEGG pathway, virulence factors and antimicrobial resistance. Furthermore, various visualization tools in the HGTree v2.0 database website provide intuitive biological insights, allowing the users to investigate their genomes of interest.

Acclimation of the photosynthetic apparatus to low light in a thermophilic Synechococcus sp. strain

Depending upon their growth responses to high and low irradiance, respectively, thermophilic Synechococcus sp. isolates from microbial mats associated with the effluent channels of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, can be described as either high-light (HL) or low-light (LL) ecotypes. Strains isolated from the bottom of the photic zone grow more rapidly at low irradiance compared to strains isolated from the uppermost layer of the mat, which conversely grow better at high irradiance. The LL-ecotypes develop far-red absorbance and fluorescence emission features after growth in LL. These isolates have a unique gene cluster that encodes a putative cyanobacteriochrome denoted LcyA, a putative sensor histidine kinase; an allophycocyanin (FRL-AP; ApcD4-ApcB3) that absorbs far-red light; and a putative chlorophyll a-binding protein, denoted IsiX, which is homologous to IsiA. The emergence of FRL absorbance in LL-adapted cells of Synechococcus sp. strain A1463 was analyzed in cultures responding to differences in light intensity. The far-red absorbance phenotype arises from expression of a novel antenna complex containing the FRL-AP, ApcD4-ApcB3, which is produced when cells were grown at very low irradiance. Additionally, the two GAF domains of LcyA were shown to bind phycocyanobilin and a [4Fe-4S] cluster, respectively. These ligands potentially enable this photoreceptor to respond to a variety of environmental factors including irradiance, redox potential, and/or oxygen concentration. The products of the gene clusters specific to LL-ecotypes likely facilitate growth in low-light environments through a process called Low-Light Photoacclimation.

Temperature and Geographic Location Impact the Distribution and Diversity of Photoautotrophic Gene Variants in Alkaline Yellowstone Hot Springs

Alkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on studying how cyanobacteria (oxygenic phototrophs) vary with temperature, sulfide, and pH, but many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. To this end, we examined the distribution of genes involved in phototrophy, carbon fixation, and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites near the upper temperature limit of photosynthesis (71ºC) in YNP using metagenome sequencing. Based on genes encoding key reaction center proteins, geographic isolation plays a larger role than temperature in selecting for distinct phototrophic Chloroflexi, while genes typically associated with autotrophy in anoxygenic phototrophs, did not have distinct distributions with temperature. Additionally, we recovered Calvin cycle gene variants associated with Chloroflexi, an alternative carbon fixation pathway in anoxygenic photoautotrophs. Lastly, we recovered several abundant nitrogen fixation gene sequences associated with Roseiflexus, providing further evidence that genes involved in nitrogen fixation in Chloroflexi are more common than previously assumed. Together, our results add to the body of work on the distribution and functional potential of phototrophic bacteria in Yellowstone National Park hot springs and support the hypothesis that a combination of abiotic and biotic factors impact the distribution of phototrophic bacteria in hot springs. Future studies of isolates and metagenome assembled genomes (MAGs) from these data and others will further our understanding of the ecology and evolution of hot spring anoxygenic phototrophs. IMPORTANCE Photosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology. While a large body of work has focused on oxygenic photosynthesis in cyanobacteria in Mushroom and Octopus Springs in Yellowstone National Park, many questions remain regarding the metabolic potential and ecology of hot spring anoxygenic phototrophs. Anoxygenic phototrophs are metabolically and taxonomically diverse, and further investigations into their physiology will lead to a deeper understanding of microbial evolution and ecology of these taxa. Here, we have quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Our results suggest that temperature >68ºC selects for distinct groups of cyanobacteria and that carbon fixation pathways associated with these taxa are likely subject to the same selective pressure. Additionally, our data suggest that phototrophic Chloroflexi genes and carbon fixation genes are largely influenced by local conditions as evidenced by our gene variant analysis. Lastly, we recovered several genes associated with potentially novel phototrophic Chloroflexi. Together, our results add to the body of work on hot springs in Yellowstone National Park and set the stage for future work on metagenome assembled genomes.

Proteomic Time-Course Analysis of the Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus aurantiacus, during the Transition from Respiration to Phototrophy

Chloroflexus aurantiacus is a filamentous anoxygenic phototrophic bacterium that grows chemotrophically under oxic conditions and phototrophically under anoxic conditions. Because photosynthesis-related genes are scattered without any gene clusters in the genome, it is still unclear how this bacterium regulates protein expression in response to environmental changes. In this study, we performed a proteomic time-course analysis of how C. aurantiacus expresses proteins to acclimate to environmental changes, namely the transition from chemoheterotrophic respiratory to photoheterotrophic growth mode. Proteomic analysis detected a total of 2520 proteins out of 3934 coding sequences in the C. aurantiacus genome from samples collected at 13 time points. Almost all proteins for reaction centers, light-harvesting chlorosomes, and carbon fixation pathways were successfully detected during the growing phases in which optical densities and relative bacteriochlorophyll c contents increased simultaneously. Combination of proteomics and pigment analysis suggests that the self-aggregation of bacteriochlorophyllide c could precede the esterification of the hydrophobic farnesyl tail in cells. Cytoplasmic subunits of alternative complex III were interchanged between oxic and anoxic conditions, although membrane-bound subunits were used for both conditions. These data highlight the protein expression dynamics of phototrophy-related genes during the transition from respiration to phototrophy.

Differential Phototactic Behavior of Closely Related Cyanobacterial Isolates from Yellowstone Hot Spring Biofilms

Phototrophic biofilms in most environments experience major changes in light levels throughout a diel cycle. Phototaxis can be a useful strategy for optimizing light exposure under these conditions, but little is known about its role in cyanobacteria from thermal springs. We examined two closely related Synechococcus isolates (Synechococcus OS-A dominates at 60 to 65°C and OS-B' at 50 to 55°C) from outflows of Octopus Spring in Yellowstone National Park. Both isolates exhibited phototaxis and photokinesis in white light, but with differences in speed and motility bias. OS-B' exhibited phototaxis toward UVA, blue, green, and red wavelengths, while OS-A primarily exhibited phototaxis toward red and green. OS-A also exhibited negative phototaxis under certain conditions. The repertoires of photoreceptors and signal transduction elements in both isolates were quite different from those characterized in other unicellular cyanobacteria. These differences in the photoresponses between OS-A and OS-B' in conjunction with in situ observations indicate that phototactic strategies may be quite versatile and finely tuned to the light and local environment. IMPORTANCE Optimizing light absorption is of paramount importance to photosynthetic organisms. Some photosynthetic microbes have evolved a sophisticated process called phototaxis to move toward or away from a light source. In many hot springs in Yellowstone National Park, cyanobacteria thrive in thick, laminated biofilms or microbial mats, where small movements can result in large changes in light exposure. We quantified the light-dependent motility behaviors in isolates representing two of the most abundant and closely related cyanobacterial species from these springs. We found that they exhibited unexpected differences in their speed, directionality, and responses to different intensities or qualities of light. An examination of their genomes revealed several variations from well-studied phototaxis-related genes. Studying these recently isolated cyanobacteria reveals that diverse phototactic strategies can exist even among close relatives in the same environment. It also provides insights into the importance of phototaxis for growth and survival in microbial biofilm communities.

Cyanobacterial Community Structure and Isolates From Representative Hot Springs of Yunnan Province, China Using an Integrative Approach

Cyanobacteria from the representative hot springs of Yunnan Province, China are explored for their diversity and community composition following an integrative approach of cultivation-independent and -dependent studies and further isolation of potential taxa for future biotechnological perspective. 16S rRNA amplicon sequencing of microbial mats in these hot springs with temperature ranging from 38 to 90°C revealed Cyanobacteria and Proteobacteria constituting a bounteous portion of the bacterial community. The combined approach of 16S rRNA amplicon sequencing and phenotypic analysis revealed the diversity of cyanobacteria (a total of 45 genera). Out of these, a total of 19 cyanobacterial taxa belonging to 6 genera and 10 species were isolated as individuals with the possibility of biotechnological utilization. These isolates were subjected to a thorough morphological study and molecular characterization using 16S rRNA gene sequencing for identification and understanding their phylogeny. The identity and phenotypic and genotypic characteristics of 7 cyanobacterial isolates are not identical to any known cyanobacterial species, generating scope for future taxonomic novelties. Preliminary experiments based on high-temperature (50°C) cultivation showed that most of the isolates were thermotolerant and suggested for their high biotechnological usage potential.

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.

An ensemble approach to the structure-function problem in microbial communities

The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.

Patterns of Relative Bacterial Richness and Community Composition in Seawater and Marine Sediment Are Robust for Both Operational Taxonomic Units and Amplicon Sequence Variants

To understand the relative influences of operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) on patterns of marine microbial diversity and community composition, we examined bacterial diversity and community composition of seawater from 12 sites in the North Atlantic Ocean and Canadian Arctic and sediment from two sites in the North Atlantic. For the seawater analyses, we included samples from three to six zones in the water column of each site. For the sediment analyses, we included over 20 sediment horizons at each of two sites. For all samples, we amplified the V4-V5 hypervariable region of the 16S ribosomal RNA (rRNA) gene. We analyzed each sample in two different ways: (i) by clustering its reads into 97%-similar OTUs and (ii) by assigning sequences to unique ASVs. OTU richness is much higher than ASV richness for every sample, but both OTUs and ASVs exhibit similar vertical patterns of relative diversity in both the water column and the sediment. Bacterial richness is highest just below the photic zone in the water column and at the seafloor in the sediment. For both OTUs and ASVs, richness estimates depend on the number of sequences analyzed. Both methods yield broadly similar community compositions for each sample at the taxonomic levels of phyla to families. While the two methods yield different richness values, broad-scale patterns of relative richness and community composition are similar with both methods.

Spirulina platensis protects against microcystin-LR-induced toxicity in rats

Microcystis aeruginosa produces an abundant cyanotoxin (microcystins (MCs) in freshwater supplies. MCs have adverse health hazards to animals and humans. Microcystin-leucine-arginine (microcystin-LR or MC-LR) is the most studied among these MCs due to their high toxicity. So, this study was designed to evaluate the possible therapeutic role of the natural algal food supplement, Spirulina platensis (SP), against MC-LR-induced toxic effects in male Wistar rats. Forty rats were randomly divided into five groups. Control and SP groups orally administered distilled water and SP (1000 mg/kg/daily), respectively, for 21 days. MC-LR group was intraperitoneally injected with MC-LR (10 μg/kg/day) for 14 days. MC-LR-SP500 and MC-LR-SP1000 groups were orally treated with SP (500 and 1000 mg/kg, respectively) for 7 days and concomitantly with MC-LR for 14 days. MC-LR induced oxidative hepatorenal damage, cardiotoxicity, and neurotoxicity greatly, which was represented by reduction of reduced glutathione content and the activities of glutathione peroxidase, catalase, and superoxide dismutase and elevation of concentrations of nitric oxide and malondialdehyde in renal, hepatic, brain, and heart tissues. In addition, it increased serum levels of urea, creatinine, tumor necrosis factor-alfa, interleukin-1beta and interleukin-6 and serum activities of alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, creatine kinase, and creatine kinase-MB. However, S. platensis restored normal levels of measured serum parameters, ameliorated MC-LR-induced oxidative damage, and normalized tissue antioxidant biomarkers. In conclusion, SP alleviated MC-induced organ toxicities by mitigating oxidative and nitrosative stress and lipid peroxidation.

Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology

Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications.

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Closed genome of the cyanobacteria Ca. P. alkaliphilum from high-pH photobioreactor

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Genetic factors lead this Phormidium to outcompete other cyanobacteria in photobioreactor

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Adaptation to high pH and alkalinity is not linked to specific genes

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Strain-level diversity contributes Ca. P. alkaliphilum success in changing conditions

A Novel Microbialite-Associated Phototrophic Chloroflexi Lineage Exhibiting a Quasi-Clonal Pattern along Depth

Chloroflexales (Chloroflexi) are typical members of the anoxygenic photosynthesizing component of microbial mats and have mostly been characterized from communities associated to hot springs. Here, we report the assembly of five metagenome-assembled genomes (MAGs) of a novel lineage of Chloroflexales found in mesophilic lithifying microbial mats (microbialites) in Lake Alchichica (Mexico). Genomic and phylogenetic analyses revealed that the bins shared 92% of their genes, and these genes were nearly identical despite being assembled from samples collected along a depth gradient (1-15 m depth). We tentatively name this lineage Candidatus Lithoflexus mexicanus. Metabolic predictions based on the MAGs suggest that these chlorosome-lacking mixotrophs share features in central carbon metabolism, electron transport, and adaptations to life under oxic and anoxic conditions, with members of two related lineages, Chloroflexineae and Roseiflexineae. Contrasting with the other diverse microbialite community members, which display much lower genomic conservation along the depth gradient, Ca. L. mexicanus MAGs exhibit remarkable similarity. This might reflect a particular flexibility to acclimate to varying light conditions with depth or the capacity to occupy a very specific spatial ecological niche in microbialites from different depths. Alternatively, Ca. L. mexicanus may also have the ability to modulate its gene expression as a function of the local environmental conditions during diel cycles in microbialites along the depth gradient.

The Thermosynechococcus Genus: Wide Environmental Distribution, but a Highly Conserved Genomic Core

Cyanobacteria thrive in diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain as well as few genes that are unique to the genus. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle-or reduced genetic complexity of hot spring habitats relative to other environments.

Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters

Autotrophic microorganisms catalyze the entry of dissolved inorganic carbon (DIC; = CO2 + HCO3- + CO32-) into the biological component of the global carbon cycle, despite dramatic differences in DIC abundance and composition in their sometimes extreme environments. "Cyanobacteria" are known to have CO2 concentrating mechanisms (CCMs) to facilitate growth under low CO2 conditions. These CCMs consist of carboxysomes, containing enzymes ribulose 1,5-bisphosphate oxygenase and carbonic anhydrase, partnered to DIC transporters. CCMs and their DIC transporters have been studied in a handful of other prokaryotes, but it was not known how common CCMs were beyond "Cyanobacteria". Since it had previously been noted that genes encoding potential transporters were found neighboring carboxysome loci, α-carboxysome loci were gathered from bacterial genomes, and potential transporter genes neighboring these loci are described here. Members of transporter families whose members all transport DIC (CHC, MDT and Sbt) were common in these neighborhoods, as were members of the SulP transporter family, many of which transport DIC. 109 of 115 taxa with carboxysome loci have some form of DIC transporter encoded in their genomes, suggesting that CCMs consisting of carboxysomes and DIC transporters are widespread not only among "Cyanobacteria", but also among members of "Proteobacteria" and "Actinobacteria".

Algal Toxic Compounds and Their Aeroterrestrial, Airborne and other Extremophilic Producers with Attention to Soil and Plant Contamination: A Review

The review summarizes the available knowledge on toxins and their producers from rather disparate algal assemblages of aeroterrestrial, airborne and other versatile extreme environments (hot springs, deserts, ice, snow, caves, etc.) and on phycotoxins as contaminants of emergent concern in soil and plants. There is a growing body of evidence that algal toxins and their producers occur in all general types of extreme habitats, and cyanobacteria/cyanoprokaryotes dominate in most of them. Altogether, 55 toxigenic algal genera (47 cyanoprokaryotes) were enlisted, and our analysis showed that besides the “standard” toxins, routinely known from different waterbodies (microcystins, nodularins, anatoxins, saxitoxins, cylindrospermopsins, BMAA, etc.), they can produce some specific toxic compounds. Whether the toxic biomolecules are related with the harsh conditions on which algae have to thrive and what is their functional role may be answered by future studies. Therefore, we outline the gaps in knowledge and provide ideas for further research, considering, from one side, the health risk from phycotoxins on the background of the global warming and eutrophication and, from the other side, the current surge of interest which phycotoxins provoke due to their potential as novel compounds in medicine, pharmacy, cosmetics, bioremediation, agriculture and all aspects of biotechnological implications in human life.

Fungi and viruses as important players in microbial mats

Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.

Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps

The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.

Novel Cyanobacterial Diversity Found in Costa Rican Thermal Springs Associated with Rincon de la Vieja and Miravalles Volcanoes: A Polyphasic Approach

Central America is one of the most important biodiversity hot spots in the world, and Costa Rican microbial communities from thermal springs are the best characterized in the isthmus. Miravalles is an inactive quaternary stratovolcano, and the Rincón de la Vieja is a unique active volcano, in whose slopes diverse hydrothermal springs, such as Las Lilas, are located. These springs harbor extensive microbial mats, whose diversity has been studied. Based on their importance as primary producers, in this study we focused on cultured cyanobacterial diversity from two geothermal environments of northern Costa Rica. Several cultural, molecular and taxonomic techniques were employed to maximize the results of a polyphasic approach. Sample collection sites were physicochemically described, and strains were isolated and characterized by light and electron microscopy. Phylogenetic analysis was performed using 16S rRNA gene sequences and amplified ribosomal DNA restriction analysis (ARDRA). Fifty-six phylotypes were isolated and classified into 21 morphotypes and identified in 14 genera, some of them might be new species within these genera. Furthermore, according to phylogenetic analysis, there are three possible new genera in our collection. Miravalles and Las Lilas thermal springs are reservoirs of novel phylogeographic lineages of phototrophic microorganisms. This study is the first report of strains that belong to the genera Gloeocapsa, Stanieria, Microseira, Klisinema and Oculatella isolated from thermal springs and growing at temperatures above 50°C. We also obtained isolates assigned to Synechococcus, Leptolyngbya spp., and Fischerella, which are considered typical strains in these environments.

Energetics of Acidianus ambivalens growth in response to oxygen availability

All life requires energy to drive metabolic reactions such as growth and cell maintenance; therefore, fluctuations in energy availability can alter microbial activity. There is a gap in our knowledge concerning how energy availability affects the growth of extreme chemolithoautotrophs. Toward this end, we investigated the growth of thermoacidophile Acidianus ambivalens during sulfur oxidation under aerobic to microaerophilic conditions. Calorimetry was used to measure enthalpy (ΔH_inc ) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔG_inc ) during incubation. In all experiments, Gibbs energy was primarily dissipated through the release of heat, which suggests enthalpy-driven growth. In microaerophilic conditions, growth was significantly more efficient in terms of biomass yield (defined as C-mol biomass per mole sulfur consumed) and resulted in lower ΔG_inc and ΔH_inc . ΔG_inc in oxygen-limited (OL) and oxygen- and CO₂ -limited (OCL) microaerophilic growth conditions resulted in averages of -1.44 × 10³  kJ/C-mol and -7.56 × 10²  kJ/C-mol, respectively, and average ΔH_inc values of -1.11 × 10⁵  kJ/C-mol and -4.43 × 10⁴  kJ/C-mol, respectively. High-oxygen experiments resulted in lower biomass yield values, an increase in ΔG_inc to -1.71 × 10⁴  kJ/C-mol, and more exothermic ΔH_inc values of -4.71 × 10⁵  kJ/C-mol. The observed inefficiency in high-oxygen conditions may suggest larger maintenance energy demands due to oxidative stresses and a preference for growth in microaerophilic environments.

Microbial Diversity of Pinnacle and Conical Microbial Mats in the Perennially Ice-Covered Lake Untersee, East Antarctica

Antarctic perennially ice-covered lakes provide a stable low-disturbance environment where complex microbially mediated structures can grow. Lake Untersee, an ultra-oligotrophic lake in East Antarctica, has the lake floor covered in benthic microbial mat communities, where laminated organo-sedimentary structures form with three distinct, sympatric morphologies: small, elongated cuspate pinnacles, large complex cones and flat mats. We examined the diversity of prokaryotes and eukaryotes in pinnacles, cones and flat microbial mats using high-throughput sequencing of 16S and 18S rRNA genes and assessed how microbial composition may underpin the formation of these distinct macroscopic mat morphologies under the same environmental conditions. Our analysis identified distinct clustering of microbial communities according to mat morphology. The prokaryotic communities were dominated by Cyanobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria. While filamentous Tychonema cyanobacteria were common in all mat types, Leptolyngbya showed an increased relative abundance in the pinnacle structures only. Our study provides the first report of the eukaryotic community structure of Lake Untersee benthic mats, which was dominated by Ciliophora, Chlorophyta, Fungi, Cercozoa, and Discicristata. The eukaryote richness was lower than for prokaryote assemblages and no distinct clustering was observed between mat morphologies. These findings suggest that cyanobacterial assemblages and potentially other bacteria and eukaryotes may influence structure morphogenesis, allowing distinct structures to form across a small spatial scale.

Fingerprinting molecular and isotopic biosignatures on different hydrothermal scenarios of Iceland, an acidic and sulfur-rich Mars analog

Detecting signs of potential extant/extinct life on Mars is challenging because the presence of organics on that planet is expected to be very low and most likely linked to radiation-protected refugia and/or preservative strategies (e.g., organo-mineral complexes). With scarcity of organics, accounting for biomineralization and potential relationships between biomarkers, mineralogy, and geochemistry is key in the search for extraterrestrial life. Here we explored microbial fingerprints and their associated mineralogy in Icelandic hydrothermal systems analog to Mars (i.e., high sulfur content, or amorphous silica), to identify potentially habitable locations on that planet. The mineralogical assemblage of four hydrothermal substrates (hot springs biofilms, mud pots, and steaming and inactive fumaroles) was analyzed concerning the distribution of biomarkers. Molecular and isotopic composition of lipids revealed quantitative and compositional differences apparently impacted by surface geothermal alteration and environmental factors. pH and water showed an influence (i.e., greatest biomass in circumneutral settings with highest supply and turnover of water), whereas temperature conditioned the mineralogy that supported specific microbial metabolisms related with sulfur. Raman spectra suggested the possible coexistence of abiotic and biomediated sources of minerals (i.e., sulfur or hematite). These findings may help to interpret future Raman or GC-MS signals in forthcoming Martian missions.

Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria

Several cyanobacterial species are dominant primary producers in hot spring microbial mats. To date, hot spring cyanobacterial taxonomy, as well as the evolution of their genomic adaptations to high temperatures, are poorly understood, with genomic information currently available for only a few dominant genera, including Fischerella and Synechococcus. To address this knowledge gap, the present study expands the genomic landscape of hot spring cyanobacteria and traces the phylum-wide genomic consequences of evolution in high temperature environments. From 21 globally distributed hot spring metagenomes, with temperatures between 32 and 75°C, 57 medium- and high-quality cyanobacterial metagenome-assembled genomes were recovered, representing taxonomic novelty for 1 order, 3 families, 15 genera and 36 species. Comparative genomics of 93 hot spring genomes (including the 57 metagenome-assembled genomes) and 66 non-thermal genomes, showed that the former have smaller genomes and a higher GC content, as well as shorter proteins that are more hydrophilic and basic, when compared to the non-thermal genomes. Additionally, the core accessory orthogroups from the hot spring genomes of some genera had a greater abundance of functional categories, such as inorganic ion metabolism, translation and post-translational modifications. Moreover, hot spring genomes showed increased abundances of inorganic ion transport and amino acid metabolism, as well as less replication and transcription functions in the protein coding sequences. Furthermore, they showed a higher dependence on the CRISPR-Cas defense system against exogenous nucleic acids, and a reduction in secondary metabolism biosynthetic gene clusters. This suggests differences in the cyanobacterial response to environment-specific microbial communities. This phylum-wide study provides new insights into cyanobacterial genomic adaptations to a specific niche where they are dominant, which could be essential to trace bacterial evolution pathways in a warmer world, such as the current global warming scenario.

Temperature impacts community structure and function of phototrophic Chloroflexi and Cyanobacteria in two alkaline hot springs in Yellowstone National Park

Photosynthetic bacteria are abundant in alkaline, terrestrial hot springs and there is a long history of research on phototrophs in Yellowstone National Park (YNP). Hot springs provide a framework to examine the ecophysiology of phototrophs in situ because they provide natural gradients of geochemistry, pH and temperature. Phototrophs within the Cyanobacteria and Chloroflexi groups are frequently observed in alkaline hot springs. Decades of research has determined that temperature constrains Cyanobacteria in alkaline hot springs, but factors that constrain the distribution of phototrophic Chloroflexi remain unresolved. Using a combination of 16S rRNA gene sequencing and photoassimilation microcosms, we tested the hypothesis that temperature would constrain the activity and composition of phototrophic Cyanobacteria and Chloroflexi. We expected diversity and rates of photoassimilation to decrease with increasing temperature. We report 16S rRNA amplicon sequencing along with carbon isotope signatures and photoassimilation from 45 to 72°C in two alkaline hot springs. We find that Roseiflexus, Chloroflexus (Chloroflexi) and Leptococcus (Cyanobacteria) operational taxonomic units (OTUs) have distinct distributions with temperature. This distribution suggests that, like phototrophic Cyanobacteria, temperature selects for specific phototrophic Chloroflexi taxa. The richness of phototrophic Cyanobacteria decreased with increasing temperature along with a decrease in oxygenic photosynthesis, whereas Chloroflexi richness and rates of anoxygenic photosynthesis did not decrease with increasing temperature, even at temperatures approaching the upper limit of photosynthesis (~72-73°C). Our carbon isotopic data suggest an increasing prevalence of the 3-hydroxypropionate pathway with decreasing temperature coincident with photoautotrophic Chloroflexi. Together these results indicate temperature plays a role in defining the niche space of phototrophic Chloroflexi (as has been observed for Cyanobacteria), but other factors such as morphology, geochemistry, or metabolic diversity of Chloroflexi, in addition to temperature, could determine the niche space of this highly versatile group.

The microalga Haematococcus lacustris (Chlorophyceae) forms natural biofilms in supralittoral White Sea coastal rock ponds

Haematococcus lacustris inhabits supralittoral rock ponds and forms, under natural conditions, biofilms including layered cyanobacterial and fermentative microbial mats. Dry mats, formed under extremely stressful conditions, contained only haematocysts. Under favorable growth conditions, modeled for dry biofilms in vitro, microalgal free-living stages were detected. Haematococcus lacustris is the microalga known for its high potential to survive under a wide range of unfavorable conditions, particularly in the supralittoral temporal rock ponds of the White Sea. Previously, we described microbial communities containing H. lacustris in this region. In many cases, they were organized into systems exhibiting complex three-dimensional structure similar to that of natural biofilms. In this study, for the first time, we clarify structural description and provide microscopic evidence that these communities of H. lacustris and bacteria are assembled into the true biofilms. There are (1) simple single layer biofilms on the surface of rocks and macrophytic algae, (2) floccules (or flocs) not attached to a surface, (3) as well as stratified (layered) biofilms, wet, and dehydrated in nature. Being involved into primary organic production, H. lacustris and cyanobacteria are located exclusively in the upper layers of stratified biofilms, where they are capable to absorb sufficient for photosynthesis amount of light. The presence of acidic polysaccharides in the extracellular matrix revealed by specific staining with ruthenium red in the H. lacustris-containing microbial communities is a biochemical evidence of biofilm formation. Meanwhile, the presence of bacterial L-form is an ultrastructural confirmation of that fact. Under favorable conditions, modeled in vitro, H. lacustris from the dry microbial mats moves to the free-living states represented by vegetative palmelloid cells and motile zoospores. Owing to the fact that inside biofilms cells of microorganisms exist under stable conditions, we consider the biofilm formation as an additional mechanism that contributes to the survival of H. lacustris in the supralittoral zone of the White Sea.

Effect of phosphate availability on biofilm formation in cooling towers

Phosphate limitation has been suggested as a preventive method against biofilms. P-limited feed water was studied as a preventive strategy against biofouling in cooling towers (CTs). Three pilot-scale open recirculating CTs were operated in parallel for five weeks. RO permeate was fed to the CTs (1) without supplementation (reference), (2) with supplementation by biodegradable carbon (P-limited) and (3) with supplementation of all nutrients (non-P-limited). The P-limited water contained ≤10 µg PO₄ l^-1. Investigating the CT-basins and coupons showed that P-limited water (1) did not prevent biofilm formation and (2) resulted in a higher volume of organic matter per unit of active biomass compared with the other CTs. Exposure to external conditions and cycle of concentration were likely factors that allowed a P concentration sufficient to cause extensive biofouling despite being the limiting compound. In conclusion, phosphate limitation in cooling water is not a suitable strategy for CT biofouling control.

Polyphosphate: A Multifunctional Metabolite in Cyanobacteria and Algae

Polyphosphate (polyP), a polymer of orthophosphate (PO4 3-) of varying lengths, has been identified in all kingdoms of life. It can serve as a source of chemical bond energy (phosphoanhydride bond) that may have been used by biological systems prior to the evolution of ATP. Intracellular polyP is mainly stored as granules in specific vacuoles called acidocalcisomes, and its synthesis and accumulation appear to impact a myriad of cellular functions. It serves as a reservoir for inorganic PO4 3- and an energy source for fueling cellular metabolism, participates in maintaining adenylate and metal cation homeostasis, functions as a scaffold for sequestering cations, exhibits chaperone function, covalently binds to proteins to modify their activity, and enables normal acclimation of cells to stress conditions. PolyP also appears to have a role in symbiotic and parasitic associations, and in higher eukaryotes, low polyP levels seem to impact cancerous proliferation, apoptosis, procoagulant and proinflammatory responses and cause defects in TOR signaling. In this review, we discuss the metabolism, storage, and function of polyP in photosynthetic microbes, which mostly includes research on green algae and cyanobacteria. We focus on factors that impact polyP synthesis, specific enzymes required for its synthesis and degradation, sequestration of polyP in acidocalcisomes, its role in cellular energetics, acclimation processes, and metal homeostasis, and then transition to its potential applications for bioremediation and medical purposes.

Analysis of the Microbiome (Bathing Biome) in Geothermal Waters from an Australian Balneotherapy Centre

Balneotherapy is an ancient practice which remains commonplace throughout the world due to perceived health benefits that include relief of arthritis, fibromyalgia and relaxation. However, bathing environments are not sterile and natural spring waters may harbour natural microbial populations that include potential pathogens. We elucidated the microbial community from water taken from the borehole, pre-filter water (chlorinated, cold and post-bathing water) and post-filter water at a commercial Australian natural hot spring bathing facility. Thiobacillus, Sphingobium and Agrobacterium were the predominant genera in samples collected from the borehole. The predominant genera changed to Sphingobium, Parvibaculum and Achromobacter following chloride treatment and Azospira replaced the Achromobacter once the water reached ambient temperature and was stored ready to be used by bathers. The microbial community changed again following use by bathers, dominated by Pseudomonas, although Sphingobium persisted. No total or faecal coliforms were observed in any of the samples except for the post-bathing water; even there, their presence was at very low concentration (2.3 cfu/mL). These results confirm the lack of pathogens present in these hot spring waters but also suggests that good management of post-bathing water is required especially if the water is used for borehole water recharge.

Unexpected Abundance and Diversity of Phototrophs in Mats from Morphologically Variable Microbialites in Great Salt Lake, Utah

Microbial mat communities are associated with extensive (∼700 km²) and morphologically variable carbonate structures, termed microbialites, in the hypersaline Great Salt Lake (GSL), Utah. However, whether the composition of GSL mat communities covaries with microbialite morphology and lake environment is unknown. Moreover, the potential adaptations that allow the establishment of these extensive mat communities at high salinity (14% to 17% total salts) are poorly understood. To address these questions, microbial mats were sampled from seven locations in the south arm of GSL representing different lake environments and microbialite morphologies. Despite the morphological differences, microbialite-associated mats were taxonomically similar and were dominated by the cyanobacterium Euhalothece and several heterotrophic bacteria. Metagenomic sequencing of a representative mat revealed Euhalothece and subdominant Thiohalocapsa populations that harbor the Calvin cycle and nitrogenase, suggesting they supply fixed carbon and nitrogen to heterotrophic bacteria. Fifteen of the next sixteen most abundant taxa are inferred to be aerobic heterotrophs and, surprisingly, harbor reaction center, rhodopsin, and/or bacteriochlorophyll biosynthesis proteins, suggesting aerobic photoheterotrophic (APH) capabilities. Importantly, proteins involved in APH are enriched in the GSL community relative to that in microbialite mat communities from lower salinity environments. These findings indicate that the ability to integrate light into energy metabolism is a key adaptation allowing for robust mat development in the hypersaline GSL.IMPORTANCE The earliest evidence of life on Earth is from organosedimentary structures, termed microbialites, preserved in 3.481-billion-year-old (Ga) rocks. Phototrophic microbial mats form in association with an ∼700-km² expanse of morphologically diverse microbialites in the hypersaline Great Salt Lake (GSL), Utah. Here, we show taxonomically similar microbial mat communities are associated with morphologically diverse microbialites across the lake. Metagenomic sequencing reveals an abundance and diversity of autotrophic and heterotrophic taxa capable of harvesting light energy to drive metabolism. The unexpected abundance of and diversity in the mechanisms of harvesting light energy observed in GSL mat populations likely function to minimize niche overlap among coinhabiting taxa, provide a mechanism(s) to increase energy yield and osmotic balance during salt stress, and enhance fitness. Together, these physiological benefits promote the formation of robust mats that, in turn, influence the formation of morphologically diverse microbialite structures that can be imprinted in the rock record.

Blue-/Green-Light-Responsive Cyanobacteriochromes Are Cell Shade Sensors in Red-Light Replete Niches

Cyanobacteriochrome (CBCRs) photoreceptors show various photochemical properties, but their ecophysiological functions remain elusive. Here, we report that the blue/green CBCRs SesA/B/C can serve as physiological sensors of cell density. Because cyanobacterial cells show lower transmittance of blue light than green light, higher cell density gives more green-light-enriched irradiance to cells. The cell-density-dependent suppression of cell aggregation under blue-/green-mixed light and white light conditions support this idea. Such a sensing mechanism may provide information about the cell position in cyanobacterial mats in hot springs, the natural habitat of Thermosynechococcus. This cell-position-dependent SesA/B/C-mediated regulation of cellular sessility (aggregation) might be ecophysiologically essential for the reorganization and growth of phototrophic mats. We also report that the green-light-induced dispersion of cell aggregates requires red-light-driven photosynthesis. Blue/green CBCRs might work as shade detectors in a different niche than red/far-red phytochromes, which may be why CBCRs have evolved in cyanobacteria.

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Blue- and green-light-sensing cyanobacteriochromes can be sensors of cell density

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They may provide information about the cell position in microbial mats

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Green-light-induced dispersion of aggregates needs red-light-driven photosynthesis

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Cyanobacteriochromes might work in a different niche than red/far-red phytochromes

The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems

Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.

Terrestrial Hot Spring Systems: Introduction

This report reviews how terrestrial hot spring systems can sustain diverse and abundant microbial communities and preserve their fossil records. Hot springs are dependable water sources, even in arid environments. They deliver reduced chemical species and other solutes to more oxidized surface environments, thereby providing redox energy and nutrients. Spring waters have diverse chemical compositions, and their outflows create thermal gradients and chemical precipitates that sustain diverse microbial communities and entomb their remnants. These environments probably were important habitats for ancient benthic microbial ecosystems, and it has even been postulated that life arose in hydrothermal systems. Thermal spring communities are fossilized in deposits of travertine, siliceous sinter, and iron minerals (among others) that are found throughout the geological record back to the oldest known well-preserved rocks at 3.48 Ga. Very few are known before the Cenozoic, but it is likely that there are many more to be found. They preserve fossils ranging from microbes to trees and macroscopic animals. Features on Mars whose morphological and spectroscopic attributes resemble spring deposits on Earth have been detected in regions where geologic context is consistent with the presence of thermal springs. Such features represent targets in the search for evidence of past life on that planet.

Vertical Distribution and Diversity of Phototrophic Bacteria within a Hot Spring Microbial Mat (Nakabusa Hot Springs, Japan)

Phototrophic microbial mats are assemblages of vertically layered microbial populations dominated by photosynthetic microorganisms. In order to elucidate the vertical distribution and diversity of phototrophic microorganisms in a hot spring-associated microbial mat in Nakabusa (Japan), we analyzed the 16S rRNA gene amplicon sequences of the microbial mat separated into five depth horizons, and correlated them with microsensor measurements of O₂ and spectral scalar irradiance. A stable core community and high diversity of phototrophic organisms dominated by the filamentous anoxygenic phototrophs, Roseiflexus castenholzii and Chloroflexus aggregans were identified together with the spectral signatures of bacteriochlorophylls (BChls) a and c absorption in all mat layers. In the upper mat layers, a high abundance of cyanobacteria (Thermosynechococcus sp.) correlated with strong spectral signatures of chlorophyll a and phycobiliprotein absorption near the surface in a zone of high O₂ concentrations during the day. Deeper mat layers were dominated by uncultured chemotrophic Chlorobi such as the novel putatively sulfate-reducing “Ca. Thermonerobacter sp.”, which showed increasing abundance with depth correlating with low O₂ in these layers enabling anaerobic metabolism. Oxygen tolerance and requirements for the novel phototroph “Ca. Chloroanaerofilum sp.” and the uncultured chemotrophic Armatimonadetes member type OS-L detected in Nakabusa hot springs, Japan appeared to differ from previously suggested lifestyles for close relatives identified in hot springs in Yellowstone National Park, USA. The present study identified various microenvironmental gradients and niche differentiation enabling the co-existence of diverse chlorophototrophs in metabolically diverse communities in hot springs.

Fischerella thermalis: a model organism to study thermophilic diazotrophy, photosynthesis and multicellularity in cyanobacteria

The true-branching cyanobacterium Fischerella thermalis (also known as Mastigocladus laminosus) is widely distributed in hot springs around the world. Morphologically, it has been described as early as 1837. However, its taxonomic placement remains controversial. F. thermalis belongs to the same genus as mesophilic Fischerella species but forms a monophyletic clade of thermophilic Fischerella strains and sequences from hot springs. Their recent divergence from freshwater or soil true-branching species and the ongoing process of specialization inside the thermal gradient make them an interesting evolutionary model to study. F. thermalis is one of the most complex prokaryotes. It forms a cellular network in which the main trichome and branches exchange metabolites and regulators via septal junctions. This species can adapt to a variety of environmental conditions, with its photosynthetic apparatus remaining active in a temperature range from 15 to 58 °C. Together with its nitrogen-fixing ability, this allows it to dominate in hot spring microbial mats and contribute significantly to the de novo carbon and nitrogen input. Here, we review the current knowledge on the taxonomy and distribution of F. thermalis, its morphological complexity, and its physiological adaptations to an extreme environment.

Variability in a permanent cyanobacterial bloom: species-specific responses to environmental drivers

Cyanobacterial blooms are characterized by intense growth of one or few species that will dominate the phytoplankton community for periods of few months to an entire year or more. However, even during persistent blooms, important seasonal changes among dominant species can be observed. Pampulha reservoir is a tropical eutrophic reservoir presenting permanent blooms. To identify the main species in this environment, a closer analysis performed by microscopy and 16S-rRNA DGGE revealed Cylindrospermopsis raciborskii as highly dominant throughout the year. The second most abundant group comprised species belonging to the Microcystis genus. They followed a well-defined seasonal pattern described by interesting species-specific ecological trends. During thermal stratification in the rainy/warmer season, C. raciborskii dominated in the water column, while Microcystis spp. were abundant at the end of the dry season, a period characterized by higher total phosphorus concentrations. Phylogenetic analyses confirmed the two dominant taxa and their seasonal trends. The results showed that cyanobacteria major controlling factors were strongly species dependent, shifting from physical/climate related (stratification) to more chemical driven (nutrients/eutrophication). Identifying these drivers is therefore essential for the understanding of the bloom dynamics and the real risks associated with each species, and to eventually adopt the most appropriate and effective management strategies.

Comparative power law analysis for the spatial heterogeneity scaling of the hot-spring microbiomes

Spatial heterogeneity is a fundamental property of any natural ecosystems, including hot spring and human microbiomes. Two important scales that spatial heterogeneity exhibits are population and community scales, and Taylor's power law (PL) and its extensions (PLEs) offer ideal quantitative models to assess population- and community-level heterogeneities. Here we analyse 165 hot spring microbiome samples at the global scale that cover a wide range of temperatures (7.5-99°C) and pH levels (3.3-9). We explore a question of fundamental importance for measuring the spatial heterogeneity of the hot-spring microbiome and further discuss their ecological implications: How do critical environmental factors such as temperature and pH influence the scaling of community spatial heterogeneity? We are particularly interested in the existence of a universal scaling model that is independent of environmental gradients. By applying PL and PLEs, we were able to obtain such scaling parameters of the hot spring at both community and population levels, which are temperature- and pH-invariant. These findings suggest that while the hot-spring microbiomes located at different regions may have different environmental conditions, they share a fundamental heterogeneity scaling parameter, analogically similar to the gravitational acceleration on Earth, which may vary slightly depending on altitude and latitude, but is invariant overall. In contrast, similar to the physics of the Moon and Earth, which have different gravitational accelerations, the hot spring and human microbiomes can have different scaling parameters as demonstrated in this study.