Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms

The control of physical and biological drivers on pelagic methane fluxes in a Patagonian fjord (Golfo Almirante Montt, Chile)

Methane fluxes from coastal waters such as fjords and the underlying control mechanisms are poorly understood. During the austral summer, we investigated a fjord in the Chilean part of Patagonia, the Golfo Almirante Montt. The study is based on measurements of methane concentration, stable carbon isotopes and the distribution and activity of methane-oxidizing bacteria in the water column, as well as oceanographic and geological observations. Our results indicate that methane is of biogenic origin and released from gas-rich sediments at the entrance of the fjord, characterized by pockmarks and gas flares. Tidal currents and turbulent mixing at the sill cause a near-surface methane plume to spread into the main fjord basin and mix with the methane- and oxygen-depleted deep water. Wind-induced mixing at the sea surface controls the methane flux from the plume into the atmosphere. The methane plume is consumed by methanotrophic bacteria of the Methylomonadaceae and Ga0077536 families, which are differently distributed along the water column. An enrichment of the characteristic gene methane monooxygenase (pmoA) in the methane-poor deep water, and a conspicuously high δ13C-CH4 signature suggest that methane-rich intrusions regularly enter the deep water, where the methane is microbially oxidized. Our interdisciplinary study offers a comprehensive insight into the complex physical and biological processes that modulate methane dynamics in fjords and thus help to better assess how methane emissions from these systems will change under anthropogenic influence.

Bacterial communities forming yellow biofilms in different cave types share a common core

The walls of different types of caves under diverse geological settings (limestone, gypsum and volcanic) are colonized by biofilms of different colors: white, yellow, pink, grey, green to dark brown, but only a few colored biofilms such as the white, yellow and grey ones have been extensively studied. However, an assessment among the microbial communities originating these biofilms in different lithologies is lacking. Here we compare the yellow biofilms from two caves, Covadura and C3, in the Gypsum Karst of Sorbas in Spain, with those from two Spanish limestone caves (Pindal and Santian), and four volcanic caves in Spain and Italy (Viento, Honda del Bejenado, Grotta del Santo, Grotta di Monte Corruccio). The structure of yellow biofilms in gypsum caves closely resembles that found in other Spanish and European limestone caves. However, volcanic cave biofilms exhibit greater variability in their microbial community structure and morphologies. Biofilms from gypsum, limestone and volcanic caves were characterized by the abundance of the genera Crossiella and the gammaproteobacterial wb1-P19. The uncultured Euzebyaceae were abundant in gypsum and Spanish volcanic caves, while in the limestone and Italian volcanic caves, they were rare or absent. Nitrospira was also abundant in limestone and volcanic caves, but not in gypsum caves. Due to the abundances of Crossiella, gammaproteobacterial wb1-P19, and uncultured Euzebyaceae, in many different ecosystems, not only in caves, as recently reported, understanding the functional diversity in which these lineages are involved seems critical. Although we have studied a limited number of yellow biofilms from caves in Spain and Italy, data from other caves in USA and Russia also point out the existence of a similarity among the most abundant members composing the structure of yellow biofilms, suggesting that they share a common core.

The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter

BACKGROUND

Moonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota.

RESULTS

Three moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development.

CONCLUSIONS

The moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.