Phylogeography of the Microcoleus vaginatus (Cyanobacteria) from three continents--a spatial and temporal characterization

Towards predicting the geographical origin of ancient samples with metagenomic data

Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.

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.

Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater

Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates. However, most MAGs do not contain 16S rRNA gene sequences, making a 16S rRNA gene-based biogeography comparison difficult. An alternative technique is to use large-scale k-mer searching to find genomes of interest in public metagenomes. This paper presents the results of k-mer based searches for 5 Antarctic cyanobacteria MAGs from Lake Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi FRX01, Microcoleus sp. MP8IB2.171, Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, and Leptolyngbyaceae cyanobacterium MP9P1.79 in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus sp. MP8IB2.171 MAG was found in a wide variety of environments, the P. pseudopriestleyi MAG was found in environments with challenging conditions, the Leptolyngbyaceae cyanobacterium MP9P1.79 MAG was only found in Antarctica, and the Leptolyngbya sp. BulkMat.35 and Pseudanabaenaceae cyanobacterium MP8IB2.15 MAGs were found in Antarctic and other cold environments. The findings based on metagenome matches and global comparisons suggest that these Antarctic cyanobacteria have distinct distribution patterns ranging from locally restricted to global distribution across the cold biosphere and other climatic zones.

Description of six new cyanobacterial species from soil biocrusts on San Nicolas Island, California, in three genera previously restricted to Brazil

As the taxonomic knowledge of cyanobacteria from terrestrial environments increases, it remains important to analyze biodiversity in areas that have been understudied to fully understand global and endemic diversity. This study was completed as part of a larger algal biodiversity study of the soil biocrusts of San Nicholas Island, California, USA. Among the taxa isolated were several new species in three genera (Atlanticothrix, Pycnacronema, and Konicacronema) which were described from, and previously restricted to, Brazil. New taxa are described herein using a polyphasic approach to cyanobacterial taxonomy that considers morphological, molecular, ecological, and biogeographical factors. Morphological data corroborated by molecular analysis including sequencing of the 16S rRNA gene, and the associated 16S-23S ITS rRNA region was used to delineate three new species of Atlanticothrix, two species of Pycnacronema, and one species of Konicacronema. The overlap of genera from San Nicolas Island and Brazil suggests that cyanobacterial genera may be widely distributed across global hemispheres, whereas the presence of distinct lineages may indicate that this is not true at the species level. Our data suggest that based upon global wind patterns, cyanobacteria in both Northern and Southern hemispheres of the Americas may have a more recent common ancestor in Northern Africa, but this common ancestry is distant enough that speciation has occurred since transatlantic dispersal.

The influence of disturbance scale on the natural recovery of biological soil crusts on the Colorado Plateau

Up to 35% of global drylands have experienced degradation due to anthropogenic impacts, including physical disturbances like trampling and soil removal. These physical disturbances can result in the loss of soil communities known as biological soil crusts (biocrusts) and the important functions they provide, such as soil stability and fertility. The reestablishment of biocrust organisms after disturbance is determined by many factors, including propagule availability, climate, and vascular plant community structure. The role of these factors in natural recovery may be intensified by the extent (or size) of a disturbance. For example, large disturbances can result in reduced propagule availability or enhanced erosion, which impact both the dispersal and establishment of biocrust organisms on disturbed soils, leading to a slower natural recovery. To test how disturbance extent impacts biocrust's natural recovery, we installed four disturbance extents by completely removing biocrust from the mineral soil in plots ranging from 0.01 m2 to 1 m2 and measured productivity and erosion resistance. We found that small disturbance extents did not differ in chlorophyll a content, total exopolysaccharide content, or soil stability after 1.5 years of natural recovery. However, the concentration of glycocalyx exopolysaccharide was higher in the smallest disturbances after the recovery period. Our results indicate that disturbances <1 m2 in scale recover at similar rates, with soil stability returning to high levels in just a few years after severe disturbance. Our findings align with prior work on biocrust natural recovery in drylands and highlight the opportunity for future work to address (1) cyanobacteria, moss, and lichen propagule dispersal; (2) rates and mechanisms of biocrust succession; and (3) the role of wind or water in determining biocrust colonization patterns as compared to lateral growth.

Distinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering

Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca2+ concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H+ antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches. This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.

Three New Plectolyngbya Species (Leptolyngbyaceae, Cyanobacteria) Isolated from Rocks and Saltern of the Republic of Korea

Thin filamentous cyanobacteria isolated from three collection sites in the Republic of Korea were suggested as three new species belonging to the genus Plectolyngbya, mainly according to their molecular characteristics. The species of Plectolyngbya, including the type species of P. hodgsonii, were cryptic species that were difficult to distinguish morphologically from each other, and had appeared in ecologically diverse habitats. P. terrestris and P. koreana were subaerophytes collected from certain black spots and soils between stone walls in Seoul, Republic of Korea. In addition, hypersaline species collected from a saltern, P. salina, shared the same halophytic feature as the P. hodgsonii from the littoral zone of a coastal lake in the Antarctic. The 16S rRNA gene phylogeny supported the monophyly of Plectolyngbya with solid support, 99% Maximum Likelihood, 98% Neighbor-Joining bootstrap support values, and 1.0 Bayesian posterior probability. The ITS sequences of P. terrestris, P. koreana, and P. salina were unique in length and nucleotide composition, with different secondary structures of D1–D1ʹ and Box-B helices, compared with those of P. hodgsonii. These results demonstrate that the proposed new Plectolyngbya species were unique in their molecular traits. Therefore, we suggest them as new species belonging to the genus Plectolyngbya with the names P. terrestris sp. nov., P. koreana sp. nov., and P. salina sp. nov.

New cyanobacterial genus Argonema is hidding in soil crusts around the world

Cyanobacteria are crucial primary producers in soil and soil crusts. However, their biodiversity in these habitats remains poorly understood, especially in the tropical and polar regions. We employed whole genome sequencing, morphology, and ecology to describe a novel cyanobacterial genus Argonema isolated from Antarctica. Extreme environments are renowned for their relatively high number of endemic species, but whether cyanobacteria are endemic or not is open to much current debate. To determine if a cyanobacterial lineage is endemic is a time consuming, elaborate, and expensive global sampling effort. Thus, we propose an approach that will help to overcome the limits of the sampling effort and better understand the global distribution of cyanobacterial clades. We employed a Sequencing Read Archive, which provides a rich source of data from thousands of environmental samples. We developed a framework for a characterization of the global distribution of any microbial species using Sequencing Read Archive. Using this approach, we found that Argonema is actually cosmopolitan in arid regions. It provides further evidence that endemic microbial taxa are likely to be much rarer than expected.

Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure

The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome‐resolved metagenomic analyses of benthic Microcoleus‐dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.5% average nucleotide identity (ANI). Most mats were dominated by one strain, but minor alleles within mats were often shared, even over large spatial distances (>300 km). Within the most common Microcoleus species, the ANI between the dominant strains within mats decreased with increasing spatial separation. However, over shorter spatial distances (tens of kilometres), mats from different subwatersheds had lower ANI than mats from the same subwatershed, suggesting that at shorter spatial distances environmental differences between subwatersheds in factors like canopy cover, conductivity, and mean annual temperature decreases ANI. Since mats in smaller creeks had similar levels of nucleotide diversity (π) as mats in larger downstream subwatersheds, within‐mat genetic diversity does not appear to depend on the downstream accumulation of upstream‐derived strains. The four‐gamete test and sequence length bias suggest recombination occurs between almost all strains within each species, even between populations separated by large distances or living in different habitats. Overall, our results show that, despite some isolation by distance and environmental conditions, sufficient gene‐flow occurs among cyanobacterial strains to prevent either driver from producing distinctive population structures across the watershed.

A novel cyanobacterial geosmin producer, revising GeoA distribution and dispersion patterns in Bacteria

Cyanobacteria are ubiquitous organisms with a relevant contribution to primary production in all range of habitats. Cyanobacteria are well known for their part in worldwide occurrence of aquatic blooms while producing a myriad of natural compounds, some with toxic potential, but others of high economical impact, as geosmin. We performed an environmental survey of cyanobacterial soil colonies to identify interesting metabolic pathways and adaptation strategies used by these microorganisms and isolated, sequenced and assembled the genome of a cyanobacterium that displayed a distinctive earthy/musty smell, typical of geosmin, confirmed by GC-MS analysis of the culture's volatile extract. Morphological studies pointed to a new Oscillatoriales soil ecotype confirmed by phylogenetic analysis, which we named Microcoleus asticus sp. nov. Our studies of geosmin gene presence in Bacteria, revealed a scattered distribution among Cyanobacteria, Actinobacteria, Delta and Gammaproteobacteria, covering different niches. Careful analysis of the bacterial geosmin gene and gene tree suggests an ancient bacterial origin of the gene, that was probably successively lost in different time frames. The high sequence similarities in the cyanobacterial geosmin gene amidst freshwater and soil strains, reinforce the idea of an evolutionary history of geosmin, that is intimately connected to niche adaptation.

Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes

In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O₂ conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.

Cyanobacterial biocrust diversity in Mediterranean ecosystems along a latitudinal and climatic gradient

Cyanobacteria are a key biotic component as primary producers in biocrusts, topsoil communities that have important roles in the functioning of drylands. Yet, major knowledge gaps exist regarding the composition of biocrust cyanobacterial diversity and distribution in Mediterranean ecosystems. We describe cyanobacterial diversity in Mediterranean semiarid soil crusts along an aridity gradient by using next-generation sequencing and bioinformatics analyses, and detect clear shifts along it in cyanobacterial dominance. Statistical analyses show that temperature and precipitation were major parameters determining cyanobacterial composition, suggesting the presence of differentiated climatic niches for distinct cyanobacteria. The responses to temperature of a set of cultivated, pedigreed strains representative of the field populations lend direct support to that contention, with psychrotolerant vs thermotolerant physiology being strain dependent, and consistent with their dominance along the natural gradient. Our results suggest a possible replacement, as global warming proceeds, of cool-adapted by warm-adapted nitrogen-fixing cyanobacteria (such as Scytonema) and a switch in the dominance of Microcoleus vaginatus by thermotolerant, novel phylotypes of bundle-forming cyanobacteria. These differential sensitivities of cyanobacteria to rising temperatures and decreasing precipitation, their ubiquity, and their low generation time point to their potential as bioindicators of global change.

Intact cell MALDI-TOF mass spectrometric analysis of Chroococcidiopsis cyanobacteria for classification purposes and identification of possible marker proteins

Cyanobacteria represent a bacterial phyllum characteristic by the ability to photosynthesize. They are potentially applicable for the production of useful compounds but may also cause poisoning or at least health problems as they can produce cyanotoxins. The introduction of a fast methodology is important not only for fundamental taxonomic purposes, but also for reliable identifications in biological studies. In this work, we have used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells to study Chroococcidiopsis strains. A library of the obtained reference mass spectra containing characteristic peptide/protein profiles was examined by software tools to characterize similarities and differences applicable for diagnostics and taxonomy. Both a similarity tree and heat map constructed from the mass spectrometric data proved consistent with 16S rRNA sequencing results. We show as novelty that a binary matrix combining ferulic and sinapinic acids performs well in acquiring reproducible mass spectra of cyanobacteria. Using the matrix solvent, a protein extraction from cells was done. After polyacrylamide gel electrophoresis, the separated protein fractions were in-gel digested and the resulting peptides analyzed by liquid chromatography coupled with tandem mass spectrometry. For the first time, photosystem protein components, phycobilisome proteins, electron transport proteins, nitrogen-metabolism and nucleic acids binding-proteins, cytochromes plus other enzymes and various uncharacterized proteins could be assigned to characteristic peaks in the mass spectrometric profiles and some of them suggested as markers in addition to 30S and 50S ribosomal proteins known from previous studies employing intact cell mass spectrometry of microorganisms.

Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core

Despite the crucial role of cyanobacteria in various ecosystems, little is known about their evolutionary histories, especially microevolutionary dynamics, because of the lack of knowledge regarding their mutation rates. Here we directly estimated cyanobacterial mutation rates based on ancient DNA analyses of ice core samples collected from Kyrgyz Republic that dates back to ~12,500 cal years before present. We successfully sequenced the 16S rRNA and 16S-23S internal transcribed spacer (ITS) region. Two cyanobacterial operational taxonomic units (OTUs) were detected from the ancient ice core samples, and these OTUs are shared with those from the modern glacier surface. The mutation rate of ITS region was estimated by comparing ancient and modern populations, and were at the magnitude of 10^-7substitutions/sites/year. By using a model selection framework, we also demonstrated that the ancient sequences from the ice sample were not contaminated from modern samples. Bayesian demographic analysis based on coalescent theory revealed that cyanobacterial population sizes increased over Asia regions during the Holocene. Thus, our results enhance our understanding of the enigmatic timescale of cyanobacterial microevolution, which has the potential to elucidate the environmental responses of cyanobacteria to the drastic climatic change events of the Quaternary.

Cyanobacterial Diversity in Biological Soil Crusts along a Precipitation Gradient, Northwest Negev Desert, Israel

Cyanobacteria occur worldwide but play an important role in the formation and primary activity of biological soil crusts (BSCs) in arid and semi-arid ecosystems. The cyanobacterial diversity in BSCs of the northwest Negev desert of Israel was surveyed at three fixed sampling stations situated along a precipitation gradient in the years 2010 to 2012. The three stations also are characterized by marked differences in soil features such as soil carbon, nitrogen, or electrical conductivity. The cyanobacterial biodiversity was analyzed by sequencing inserts of clone libraries harboring partial 16S rRNA gene sequences obtained with cyanobacteria-specific primers. Filamentous, non-diazotrophic strains (subsection III), particularly Microcoleus-like, dominated the cyanobacterial community (30% proportion) in all years. Specific cyanobacterial groups showed increased (e.g., Chroococcidiopsis, Leptolyngbya, and Nostoc strains) or decreased (e.g., unicellular strains belonging to the subsection I and Scytonema strains) abundances with declining water availability at the most arid, southern station, whereas many cyanobacterial strains were frequently found in the soils of all three stations. The cyanobacterial diversity at the three sampling stations appears dependent on the available precipitation, whereas the differences in soil chemistry were of lower importance.

Phylogenetic analysis of cultivation-resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum, Nostocales, Cyanobacteria) using single-cell and filament sequencing of environmental samples

Molecular assessment of a large portion of traditional cyanobacterial taxa has been hindered by the failure to isolate and grow them in culture. In this study, we developed an optimized protocol for single cell/filament isolation and 16S rRNA gene sequencing of terrestrial cyanobacteria with large mucilaginous sheaths, and applied it to determine the phylogenetic position of typical members of the genera Petalonema and Stigonema. A methodology based on a glass-capillary isolation technique and a semi-nested PCR protocol enabled reliable sequencing of the 16S rRNA gene from all samples analyzed. Ten samples covering seven species of Stigonema from Europe, North and Central America, and Hawaii, and the type species of Petalonema from Slovakia were sequenced. Contrary to some previous studies, which proposed a relationship with heteropolar nostocalean cyanobacteria, Petalonema appeared to belong to the family Scytonemataceae. Analysis of Stigonema specimens recovered a unique coherent phylogenetic cluster, substantially broadening our knowledge of the molecular diversity within this genus. Neither the uni- to biseriate species nor the multiseriate species formed monophyletic subclusters within the genus. Typical multiseriate species of Stigonema clustered in a phylogenetic branch derived from uni- to biseriate S. ocellatum Thuret ex Bornet & Flahault in our analysis, suggesting that species with more complex thalli may have evolved from the more simple ones. We propose the technique tested in this study as a promising tool for a future revision of the molecular taxonomy in cyanobacteria.

Synechococcus: 3 billion years of global dominance

Cyanobacteria are among the most important primary producers on the Earth. However, the evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macro-organisms and an undersampling of sequenced genomes. Thus, we present a new genome of a Synechococcus-like cyanobacterium from a novel evolutionary lineage. Further, we analyse all existing 16S rRNA sequences and genomes of Synechococcus-like cyanobacteria. Chronograms showed extremely polyphyletic relationships in Synechococcus, which has not been observed in any other cyanobacteria. Moreover, most Synechococcus lineages bifurcated after the Great Oxidation Event, including the most abundant marine picoplankton lineage. Quantification of horizontal gene transfer among 70 cyanobacterial genomes revealed significant differences among studied genomes. Horizontal gene transfer levels were not correlated with ecology, genome size or phenotype, but were correlated with the age of divergence. All findings were synthetized into a novel model of cyanobacterial evolution, characterized by serial convergence of the features, that is multicellularity and ecology.