Nitrogen fixation in microbial mat and stromatolite communities from Cuatro Cienegas, Mexico

Spatial distribution of PAHs and microbial communities in intertidal sediments of the Pearl River Estuary, South China

The exploration of sediment pollution caused by PAHs and its impact on microbial communities can provide valuable insights for the remediation of sediments. The spatial distribution of PAHs and their impact on the microbial community within the Pearl River Estuary were investigated in this study. The findings revealed that the total concentration ranges of 16 PAHs were between 24.26 and 3075.93 ng/g, with naphthalene, fluorene, and phenanthrene potentially exerting adverse biological effects. More PAHs were found to accumulate in subsurface sediments, and their average accumulation rates gradually decreased as the number of rings in PAHs increased, ranging from 180 % for 2-ring to 36 % for 6-ring. The phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi were found to dominate both surface and subsurface sediments The correlation between microbial genera and PAHs contents was weak in sediments with low levels of PAHs contamination, while a more significant positive relationship was observed in sediments with high levels of PAHs contamination. The physicochemical properties of sediments, such as pH, soil structure and Cu significantly influence bacterial community composition in highly contaminated sediments. Additionally, the network analysis revealed that certain bacterial genera, including Novosphingobium, Robiginitalea and Synechococcus_CC9902, played a pivotal role in the degradation of PAHs. These findings are significant in comprehending the correlation between bacterial communities and environmental factors in intertidal ecosystems, and establish a scientific foundation for bioremediation of intertidal zones.

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert

We describe the metagenome composition, community functional annotation, and prokaryote diversity in calcareous stromatolites from a dry stream bed of the San Felipe Creek in the Anza Borrego Desert. Analyses show a community capable of nitrogen fixation, assimilatory nitrate reduction, biofilm formation, quorum sensing, and potential thick-walled akinete formation for desiccation resistance.

A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico

Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.

Thermal Stability of (Bio)Carbonates: A Potential Signature for Detecting Life on Mars?

The environmental conditions that prevail on the surface of Mars (i.e., high levels of radiation and oxidants) are not favorable for the long-term preservation of organic compounds on which all strategies for finding life on Mars have been based to date. Since life commonly produces minerals that are considered more resilient, the search for biominerals could constitute a promising alternative approach. Carbonates are major biominerals on Earth, and although they have not been detected in large amounts at the martian surface, recent observations show that they could constitute a significant part of the inorganic component in the martian soil. Previous studies have shown that calcite and aragonite produced by eukaryotes thermally decompose at temperatures 15°C lower than those of their abiotic counterparts. By using carbonate concretions formed by microorganisms, we find that natural and experimental carbonates produced by prokaryotes decompose at 28°C below their abiotic counterparts. The study of this sample set serves as a proof of concept for the differential thermal analysis approach to distinguish abiotic from bio-related carbonates. This difference in carbonate decomposition temperature can be used as a first physical evidence of life on Mars to be searched by in situ space exploration missions with the resolution and the technical constraints of the available onboard instruments.

Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds

Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline, the former being morphologically and structurally similar to fossilized phosphatic stromatolites formations. Using assembled shotgun metagenomic analysis, we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteria phylum. We identified functional gene sets in genomic bins conserved across two geographically isolated stromatolite formations, which included relatively high copy numbers of genes involved in the reduction of nitrates and phosphatic compounds. Additionally, we found little evidence of Archaeal species in these stromatolites, suggesting that they may not play an important role in peritidal stromatolite formations, as proposed for hypersaline formations.

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.

Multiple evaluation of the potential toxic effects of sediments and biota collected from an oil-polluted area around Abu Ali Island, Saudi Arabia, Arabian Gulf

After the Gulf War Oil Spill, there have been many investigations about distributions of oil-derived pollutants nearby areas, but lacking in ecotoxicological assessment. We evaluated the potential toxicity of asphalt mats, sediments, and biota (polychaetes, chitons, snapping shrimps, and crabs) by combining two bioassays (H4IIE-luc and Vibrio fischeri) and in situ microbial community (eDNA). Samples were collected from Abu Ali Island, and organic extracts were bioassayed and further fractionated according to the chemical polarity using silica gel column. Great aryl hydrocarbon receptor (AhR)-mediated potencies and inhibition of bioluminescence were mainly found in aromatics (F2) and saturates (F1) fractions of asphalt mat and sediments, respectively, while great toxicological responses in biota samples were found in resins and polar (F3) fraction. We also confirmed that potential toxicities of biota were species-specific; great AhR-mediated potencies were found in polychaetes and great bioluminescence inhibitions were found in crabs. In microbial communities, most genera (up to 90%) were associated with polycyclic aromatic hydrocarbons (PAHs)-degrading bacteria, supporting that PAHs are the primary stressors of the benthic community around Abu Ali Island. The present study provides useful information on the contamination status, risk assessment of environmental matrices and benthic organisms in Abu Ali Island.

Metagenome of Acropora palmata coral rubble: Potential metabolic pathways and diversity in the reef ecosystem

Over the past 30 years, the stony coral Acropora palmata has experienced an excessive loss of individuals showing few signs of recovery throughout the Mexican Caribbean, resulting in long stretches of coral rubble structures. When the coral dies, the skeleton begins to be colonized by algae, sponges, virus, bacteria and other microorganisms, forming a new community. Here we analyze, using a metagenomic approach, the diversity and biogeochemical cycles associated to coral rubble in La Bocana (Puerto Morelos, QRoo, Mexico). This study provides the first broad characterization of coral rubble associated communities and their role in biogeochemical cycling, suggesting a potential view of a world where coral reefs are no longer dominated by corals.

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.

Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient

Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.

Nitrogen fixation in a non-heterocystous cyanobacterial mat from a mountain river

In situ nitrogen fixation was investigated in a cyanobacterial mat growing on the bed of rocks of the Muga River, Spain. The filamentous non-heterocystous cyanobacterium Schizothrix dominated the mat, showing nitrogenase activity in the light at similar rates to those found in nearby heterocystous Rivularia colonies. N2 fixation in the light was significantly increased by an inhibitor of PSII and oxygen evolution, DCMU (3-[3,4-dichlorophenyl]-1,1-dimethylurea), and anaerobic conditions. However, no nitrogenase activity was found in the dark. Addition of fructose as a respiratory substrate induced nitrogenase activity in samples incubated under aerobic conditions in the dark but not in anaerobic conditions. Microelectrode oxygen profiles showed internal microaerobic microzones where nitrogen fixation might concentrate. Analyses of the 16S rRNA gene revealed only the presence of sequences belonging to filamentous non-heterocystous cyanobacteria. nifH gene diversity showed that the major phylotypes also belonged to this group. One of the three strains isolated from the Schizothrix mat was capable of fixing N2 and growing in the absence of combined N. This was consistent with the nifH gene analysis. These results suggest a relevant contribution of non-heterocystous cyanobacteria to nitrogen fixation in these mats.

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.

Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling

Microbialites are sedimentary deposits formed by the metabolic interactions of microbes and their environment. These lithifying microbial communities represent one of the oldest ecosystems on Earth, yet the molecular mechanisms underlying the function of these communities are poorly understood. In this study, we used comparative metagenomic and metatranscriptomic analyses to characterize the spatial organization of the thrombolites of Highborne Cay, The Bahamas, an actively forming microbialite system. At midday, there were differences in gene expression throughout the spatial profile of the thrombolitic mat with a high abundance of transcripts encoding genes required for photosynthesis, nitrogen fixation and exopolymeric substance production in the upper three mm of the mat. Transcripts associated with denitrification and sulfate reduction were in low abundance throughout the depth profile, suggesting these metabolisms were less active during midday. Comparative metagenomics of the Bahamian thrombolites with other known microbialite ecosystems from across the globe revealed that, despite many shared core pathways, the thrombolites represented genetically distinct communities. This study represents the first time the metatranscriptome of living microbialite has been characterized and offers a new molecular perspective on those microbial metabolisms, and their underlying genetic pathways, that influence the mechanisms of carbonate precipitation in lithifying microbial mat ecosystems.

The discovery of stromatolites developing at 3570 m above sea level in a high-altitude volcanic lake Socompa, Argentinean Andes

We describe stromatolites forming at an altitude of 3570 m at the shore of a volcanic lake Socompa, Argentinean Andes. The water at the site of stromatolites formation is alkaline, hypersaline, rich in inorganic nutrients, very rich in arsenic, and warm (20-24°C) due to a hydrothermal input. The stromatolites do not lithify, but form broad, rounded and low-domed bioherms dominated by diatom frustules and aragonite micro-crystals agglutinated by extracellular substances. In comparison to other modern stromatolites, they harbour an atypical microbial community characterized by highly abundant representatives of Deinococcus-Thermus, Rhodobacteraceae, Desulfobacterales and Spirochaetes. Additionally, a high proportion of the sequences that could not be classified at phylum level showed less than 80% identity to the best hit in the NCBI database, suggesting the presence of novel distant lineages. The primary production in the stromatolites is generally high and likely dominated by Microcoleus sp. Through negative phototaxis, the location of these cyanobacteria in the stromatolites is controlled by UV light, which greatly influences their photosynthetic activity. Diatoms, dominated by Amphora sp., are abundant in the anoxic, sulfidic and essentially dark parts of the stromatolites. Although their origin in the stromatolites is unclear, they are possibly an important source of anaerobically degraded organic matter that induces in situ aragonite precipitation. To the best of our knowledge, this is so far the highest altitude with documented actively forming stromatolites. Their generally rich, diverse and to a large extent novel microbial community likely harbours valuable genetic and proteomic reserves, and thus deserves active protection. Furthermore, since the stromatolites flourish in an environment characterized by a multitude of extremes, including high exposure to UV radiation, they can be an excellent model system for studying microbial adaptations under conditions that, at least in part, resemble those during the early phase of life evolution on Earth.

Molecular characterization of potential nitrogen fixation by anaerobic methane-oxidizing archaea in the methane seep sediments at the number 8 Kumano Knoll in the Kumano Basin, offshore of Japan

The potential for microbial nitrogen fixation in the anoxic methane seep sediments in a mud volcano, the number 8 Kumano Knoll, was characterized by molecular phylogenetic analyses. A total of 111 of the nifH (a gene coding a nitrogen fixation enzyme, Fe protein) clones were obtained from different depths of the core sediments, and the phylogenetic analysis of the clones indicated the genetic diversity of nifH genes. The predominant group detected (methane seep group 2), representing 74% of clonal abundance, was phylogenetically related to the nifH sequences obtained from the Methanosarcina species but was most closely related to the nifH sequences potentially derived from the anoxic methanotrophic archaea (ANME-2 archaea). The recovery of the nif gene clusters including the nifH sequences of the methane seep group 2 and the subsequent reverse transcription-PCR detection of the nifD and nifH genes strongly suggested that the genetic components of the gene clusters would be operative for the in situ assimilation of molecular nitrogen (N(2)) by the host microorganisms. DNA-based quantitative PCR of the archaeal 16S rRNA gene, the group-specific mcrA (a gene encoding the methyl-coenzyme M reductase alpha subunit) gene, and the nifD and nifH genes demonstrated the similar distribution patterns of the archaeal 16S rRNA gene, the mcrA groups c-d and e, and the nifD and nifH genes through the core sediments. These results supported the idea that the anoxic methanotrophic archaea ANME-2c could be the microorganisms hosting the nif gene clusters and could play an important role in not only the in situ carbon (methane) cycle but also the nitrogen cycle in subseafloor sediments.

Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico

Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites.

The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment

The Cuatro Ciénegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico) hosts a wide diversity of microorganisms contained within springs thought to be geomorphological relics of an ancient sea. A major question remaining to be answered is whether bacteria from CCB are ancient marine bacteria that adapted to an oligotrophic system poor in NaCl, rich in sulfates, and with extremely low phosphorus levels (<0.3 microM). Here, we report the complete genome sequence of Bacillus coahuilensis, a sporulating bacterium isolated from the water column of a desiccation lagoon in CCB. At 3.35 Megabases this is the smallest genome sequenced to date of a Bacillus species and provides insights into the origin, evolution, and adaptation of B. coahuilensis to the CCB environment. We propose that the size and complexity of the B. coahuilensis genome reflects the adaptation of an ancient marine bacterium to a novel environment, providing support to a "marine isolation origin hypothesis" that is consistent with the geology of CCB. This genomic adaptation includes the acquisition through horizontal gene transfer of genes involved in phosphorous utilization efficiency and adaptation to high-light environments. The B. coahuilensis genome sequence also revealed important ecological features of the bacterial community in CCB and offers opportunities for a unique glimpse of a microbe-dominated world last seen in the Precambrian.