Polyphasic approach using multilocus analyses supports the establishment of the new aerophytic cyanobacterial genus Pycnacronema (Coleofasciculaceae, Oscillatoriales)

Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region

The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.

Two new species of Dulcicalothrix (Nostocales, Cyanobacteria) from India and erection of Brunnivagina gen. nov., with observations on the problem of using multiple ribosomal operons in cyanobacterial taxonomy

Two new species of Dulcicalothrix, D. adhikaryi sp. nov. and D. iyengarii sp. nov., were discovered in India and are characterized and described in accordance with the rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). As a result of phylogenetic analysis, Calothrix elsteri is reassigned to Brunnivagina gen. nov. During comparison with all Dulcicalothrix for which sequence data were available, we observed that the genus has six ribosomal operons in three orthologous types. Each of the three orthologs could be identified based upon indels occurring in the D1-D1' helix sequence in the ITS rRNA region between the 16S and 23S rRNA genes, and in these three types, there were operons containing ITS rRNA regions with and without tRNA genes. Examination of complete genomes in Dulcicalothrix revealed that, at least in the three strains for which complete genomes are available, there are five ribosomal operons, two with tRNA genes and three with no tRNA genes in the ITS rRNA region. Internal transcribed spacer rRNA regions have been consistently used to differentiate species, both on the basis of secondary structure and percent dissimilarity. Our findings call into question the use of ITS rRNA regions to differentiate species in the absence of efforts to obtain multiple operons of the ITS rRNA region through cloning or targeted PCR amplicons. The ITS rRNA region data for Dulcicalothrix is woefully incomplete, but we provide herein a means for dealing with incomplete data using the polyphasic approach to analyze diverse molecular character sets. Caution is urged in using ITS rRNA data, but a way forward through the complexity is also proposed.

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.

Description of four new filamentous cyanobacterial taxa from freshwater habitats in the Azores Archipelago

Simple filamentous cyanobacteria comprise a diverse and polyphyletic group of species, primarily in the orders Leptolyngbyales and Oscillatoriales, that need more sampling to improve their taxonomy. Oceanic islands, such as the Azores archipelago, present unique habitats and biogeographic conditions that harbor an unknown range of diversity of microorganisms. Filamentous cyanobacteria isolated from aquatic habitats in the Azores and maintained in the BACA culture collection were described using morphology, both light and transmission electron microscopy, ecology, and genetic data of the 16S rRNA gene sequences and 16S-23S Internal Transcribed Spacer (ITS) rRNA region secondary structure. Our analyses revealed two new monophyletic genera: Tumidithrix elongata gen. sp. nov. (Pseudanabaenaceae) and Radiculonema aquaticum gen. sp. nov. (Leptolyngbyaceae). In addition, two new species Leptodesmis lacustris sp. nov. (Leptolyngbyaceae) and Pycnacronema lacustrum sp. nov. (Wilmottiaceae) are reported as the first aquatic species for these genera. The description of these new taxa and the genetic study of an isolate of Leptodesmis alaskaensis from the Azores followed the polyphasic approach, identifying diacritical features. Our results reinforce the need for taxonomic studies on cyanobacteria from less-studied habits and geographic regions, which have a potential for new taxa description.

Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert

Introduction

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

Methods

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

Results

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

Discussion

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

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

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

The Compositionally Distinct Cyanobacterial Biocrusts From Brazilian Savanna and Their Environmental Drivers of Community Diversity

The last decade was marked by efforts to define and identify the main cyanobacterial players in biological crusts around the world. However, not much is known about biocrusts in Brazil’s tropical savanna (cerrado), despite the existence of environments favorable to their development and ecological relevance. We examined the community composition of cyanobacteria in biocrusts from six sites distributed in the Southeast of the country using high throughput sequencing of 16S rRNA and phylogenetic placement in the wider context of biocrusts from deserts. Sequences ascribable to 22 genera of cyanobacteria were identified. Although a significant proportion of sequences did not match those of known cyanobacteria, several clades of Leptolyngbya and Porphyrosiphon were found to be the most abundant. We identified significant differences in dominance and overall composition among the cerrado sites, much larger than within-site variability. The composition of cerrado cyanobacterial communities was distinct from those known in biocrusts from North American deserts. Among several environmental drivers considered, the opposing trend of annual precipitation and mean annual temperature best explained the variability in community composition within Brazilian biocrusts. Their compositional uniqueness speaks of the need for dedicated efforts to study the ecophysiology of tropical savanna biocrust and their roles in ecosystem function for management and preservation.