Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr's Lake, the Bahamas

Integration of multi-omics data to elucidate keystone unknown taxa within microbialite-forming ecosystems

Microbes continually shape Earth's biochemical and physical landscapes by inhabiting diverse metabolic niches. Despite the important role microbes play in ecosystem functioning, most microbial species remain unknown highlighting a gap in our understanding of structured complex ecosystems. To elucidate the relevance of these unknown taxa, often referred to as "microbial dark matter," the integration of multiple high throughput sequencing technologies was used to evaluate the co-occurrence and connectivity of all microbes within the community. Since there are no standard methodologies for multi-omics integration of microbiome data, we evaluated the abundance of "microbial dark matter" in microbialite-forming communities using different types meta-omic datasets: amplicon, metagenomic, and metatranscriptomic sequencing previously generated for this ecosystem. Our goal was to compare the community structure and abundances of unknown taxa within the different data types rather than to perform a functional characterization of the data. Metagenomic and metatranscriptomic data were input into SortMeRNA to extract 16S rRNA gene reads. The output, as well as amplicon sequences, were processed through QIIME2 for taxonomy analysis. The R package mdmnets was utilized to build co-occurrence networks. Most hubs presented unknown classifications, even at the phyla level. Comparisons of the highest scoring hubs of each data type using sequence similarity networks allowed the identification of the most relevant hubs within the microbialite-forming communities. This work highlights the importance of unknown taxa in community structure and proposes that ecosystem network construction can be used on several types of data to identify keystone taxa and their potential function within microbial ecosystems.

Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes

Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.

Using Molecular Tools to Understand Microbial Carbonates

Here we review the application of molecular biological approaches to mineral precipitation in modern marine microbialites. The review focuses on the nearly two decades of nucleotide sequencing studies of the microbialites of Shark Bay, Australia; and The Bahamas. Molecular methods have successfully characterized the overall community composition of mats, pinpointed microbes involved in key metabolisms, and revealed patterns in the distributions of microbial groups and functional genes. Molecular tools have become widely accessible, and we can now aim to establish firmer links between microbes and mineralization. Two promising future directions include “zooming in” to assess the roles of specific organisms, microbial groups, and surfaces in carbonate biomineralization and “zooming out” to consider broader spans of space and time. A middle ground between the two can include model systems that contain representatives of important microbial groups, processes, and metabolisms in mats and simplify hypothesis testing. These directions will benefit from expanding reference datasets of marine microbes and enzymes and enrichments of representative microbes from mats. Such applications of molecular tools should improve our ability to interpret ancient and modern microbialites and increase the utility of these rocks as long-term recorders of microbial processes and environmental chemistry.

Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.

Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern

The solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually different microbial mats (termed 'white' and 'green') developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in different vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chloroflexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon and nitrogen isotopic compositions determined from both mat samples showed that the δ13Corg and δ15Norg values increased slightly with depth, ranging from - 16.42 to - 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profile followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. The results and discussions presented here by merging culture-independent studies, predictive metabolic analyses and isotopic characterization, provide a collective strategy to understand the compositional and functional characteristics of microbial mats in saline environments.

The microbiome of modern microbialites in Bacalar Lagoon, Mexico

Microbialites are highly diverse microbial communities that represent modern examples of the oldest life forms, stromatolites (dated >3.7 Ga). Bacalar Lagoon, in Mexico, harbors the largest freshwater microbialite occurrences of the world; yet diverse anthropogenic activities are changing the oligotrophic conditions of the lagoon. The objective of this work was to perform a spatial exploration of the microbialites of Bacalar Lagoon, analyze their prokaryote diversity, following a high throughput sequencing approach of the V4 region of the 16S rDNA, and correlate to the environmental parameters that influence the structure of these communities. The results indicate the presence of microbialites throughout the periphery of the lagoon. The microbiome of the microbialites is composed primarily of Proteobacteria (40-80%), Cyanobacteria (1-11%), Bacteroidetes (7-8%), Chloroflexi (8-14%), Firmicutes (1-23%), Planctomycetes (1-8%), and Verrucomicrobia (1-4%). Phylogenetic distance analyses suggests two distinct groups of microbialites associated with regions in the lagoon that have differences in their environmental parameters, including soluble reactive silicate (in the north), bicarbonates and available forms of nitrogen (ammonium, nitrates and nitrites) (in the south). These microbialite groups had differences in their microbiome composition associated to strong anthropogenic pressure on water quality (agriculture, landfill leachate, lack of water treatment infrastructure and intensive tourism), which were related to a loss of microbial diversity.

Correlation of bio-optical properties with photosynthetic pigment and microorganism distribution in microbial mats from Hamelin Pool, Australia

Microbial mats and stromatolites are widespread in Hamelin Pool, Shark Bay, however the phototrophic capacity of these systems is unknown. This study has determined the optical properties and light-harvesting potential of these mats with light microsensors. These characteristics were linked via a combination of 16S rDNA sequencing, pigment analyses and hyperspectral imaging. Local scalar irradiance was elevated over the incident downwelling irradiance by 1.5-fold, suggesting light trapping and strong scattering by the mats. Visible light (400-700 nm) penetrated to a depth of 2 mm, whereas near-infrared light (700-800 nm) penetrated to at least 6 mm. Chlorophyll a and bacteriochlorophyll a (Bchl a) were found to be the dominant photosynthetic pigments present, with BChl a peaking at the subsurface (2-4 mm). Detailed 16S rDNA analyses revealed the presence of putative Chl f-containing Halomicronema sp. and photosynthetic members primarily decreased from the mat surface down to a depth of 6 mm. Data indicated high abundances of some pigments and phototrophic organisms in deeper layers of the mats (6-16 mm). It is proposed that the photosynthetic bacteria present in this system undergo unique adaptations to lower light conditions below the mat surface, and that phototrophic metabolisms are major contributors to ecosystem function.

Methods for extracting 'omes from microbialites

Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Additionally, several commercial kits have been used to improve DNA and total RNA extraction. This minireview presents different methods applied for DNA and RNA extraction from microbialites and discusses their advantages and disadvantages. Moreover, extraction of all 'omes (DNA, RNA, Protein, Lipids, polar metabolites) using multiomic extraction methods (MPlex), as well as the state of art for extraction of viruses from microbialites, are also discussed.

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (C_org), nitrogen and C_org:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.

Stromatolites on the rise in peat-bound karstic wetlands

Stromatolites are the oldest evidence for life on Earth, but modern living examples are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7.0-7.9) enclaves within an otherwise uniformly acidic organosol terrain. The freshwater emerging from the springs is Ca-HCO3 dominated and water temperatures show no evidence of geothermal heating. Using 16 S rRNA gene clone library analysis we revealed that the bacterial community is dominated by Cyanobacteria, Alphaproteobacteria and an unusually high proportion of Chloroflexi, followed by Armatimonadetes and Planctomycetes, and is therefore unique compared to other living examples. Macroinvertebrates are sparse and snails in particular are disadvantaged by the development of debilitating accumulations of carbonate on their shells, corroborating evidence that stromatolites flourish under conditions where predation by metazoans is suppressed. Our findings constitute a novel habitat for stromatolites because cool-temperate freshwater wetlands are not a conventional stromatolite niche, suggesting that stromatolites may be more common than previously thought.

A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses

Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems. Key Words: Thrombolites-Microbial diversity-Metagenome-Stable isotopes-Microbialites. Astrobiology 17, 413-430.

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis

Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites.