Molecular ecology of microbial mats

Abstract

Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep and fluctuating physicochemical microgradients, that are the result of the ever changing environmental conditions and of the microorganisms' own activities, give rise to a plethora of potential niches resulting in the formation of one of the most diverse microbial ecosystems known to date. For several decades, microbial mats have been studied extensively and more recently molecular biological techniques have been introduced that allowed assessing and investigating the diversity and functioning of these systems. These investigations also involved metagenomics analyses using high-throughput DNA and RNA sequencing. Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring, and hypersaline). We also present a comparison of the available metagenomic data sets from mats emphasizing the major differences between them as well as elucidating the overlap in overall community composition.

From the Cell to the Ecosystem: The Physiological Evolution of Symbiosis

“…In marine ecosystems, members of this phylum decompose highmolecular-mass dissolved organic matter . Chloroflexi, Chlorobi, Acidobacteria, and Actinobacteria are minor phyla in hypersaline mats, but they contribute significantly to carbon and sulfur cycling (Bolhuis et al 2014). The presence in microbial mats of very diverse and stable populations of spirochetes suggests their involvement in a well-integrated metabolic symbiosis (i.e., permanent physiological cooperation) with other specialized populations in the mats, where they maintain a coordinated functional and stable community (Berlanga et al 2008).…”

Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals

“…This conserved interdependence of Roseofilum and heterotrophic bacteria may be linked to metabolic requirements and may explain why this cyanobacterium is found within apparently healthy coral microbiomes (Meyer et al, 2016). In many ways, BBD consortia resemble microbial mats found in tropical lagoons (Echenique-Subiabre et al, 2015), mangroves (Guidi-Rotani et al, 2014), and modern marine stromatolites (Ruvindy et al, 2016) that are characterized by steep physicochemical gradients and the presence of Cyanobacteria, Bacteroidetes, and Proteobacteria (especially Alpha-, Delta-, and Gammaproteobacteria; Bolhuis et al, 2014). With the large size of filamentous cyanobacteria relative to other bacterial cells, their production of exopolysaccharides that consolidate the mat, and their critical roles in converting inorganic carbon, nitrogen, and sulfur to organic forms, Cyanobacteria are the pioneering microorganisms of microbial mats (Bolhuis et al, 2014).…”

“…In many ways, BBD consortia resemble microbial mats found in tropical lagoons (Echenique-Subiabre et al, 2015), mangroves (Guidi-Rotani et al, 2014), and modern marine stromatolites (Ruvindy et al, 2016) that are characterized by steep physicochemical gradients and the presence of Cyanobacteria, Bacteroidetes, and Proteobacteria (especially Alpha-, Delta-, and Gammaproteobacteria; Bolhuis et al, 2014). With the large size of filamentous cyanobacteria relative to other bacterial cells, their production of exopolysaccharides that consolidate the mat, and their critical roles in converting inorganic carbon, nitrogen, and sulfur to organic forms, Cyanobacteria are the pioneering microorganisms of microbial mats (Bolhuis et al, 2014). Likewise, Roseofilum is the engineer of the black band consortium, creating a narrow polymicrobial band on the surface of reef-building corals (Miller and Richardson, 2011; Casamatta et al, 2012; Richardson et al, 2014).…”

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

“…Serpentinization is a mineral hydration process that produces H 2 , CH 4 , alkaline fluids, and low-molecular-weight organic compounds and has been suggested to constitute a source of carbon and energy for chemosynthetic life (1–9). Ultramafic, iron-bearing rocks generate H 2 by splitting water concomitant with iron oxidation.…”

“…Ultramafic, iron-bearing rocks generate H 2 by splitting water concomitant with iron oxidation. Subsequently, CH 4 is synthesized via a Fischer-Tropsch-type reaction in which H 2 reduces CO 2 to CH 4 (1–15). Low-temperature abiotic gas seepages on land, such as the Chimaera seep in Çıralı, Antalya Gulf, Turkey, have been identified at only a few sites on Earth (1, 16).…”