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Due to its extreme conditions, microbial life in the Atacama Desert is known to survive in well-protected micro-habitats (hypolithic, endolithic, etc.), but rarely directly exposed to the environment, that is, epilithic habitats. Here we report a unique site, La Portada, a cliff confronting the Pacific Ocean in the Coastal Range of this desert, in which the constant input of water provided by the sea spray allows for the growth of a black-colored epilithic subaerial microbial ecosystem. Formed by a complex community of halophilic microorganisms belonging to the three domains of life, this ecosystem displays the typical three-dimensional structure of benthic microbialites, coherent with the presence of a diversity of cyanobacteria (including species from the genera that are known to form them), a constant high water activity and an ample availability of carbonate ions. From these microbialites we isolated Hortae werneckii, a fungal species which by producing melanin, not only explains the dark color of these microbialites, but may also play the role of protecting the whole community from extreme UV radiation. A number of biosignatures not only confirmed sea spray as the main source of water, but also suggests that one place to consider for the search of evidences of life on Mars would be on the paleo-coastlines that surrounded vanished oceans such as that on Aeolis Dorsa.

Schembri, S. and Zammit, G., 2022. The biodiversity of epilithic microalgal communities colonising a central Mediterranean coastline. Journal of Coastal Research, 38(2), 249–260. Coconut Creek (Florida), ISSN 0749-0208. Microbial communities colonise the coastal ecosystem around the Maltese islands. However, such communities are understudied, both in Malta and in the central Mediterranean. This research aims to increase current knowledge about the biodiversity of phototrophic communities growing along a central Mediterranean rocky shoreline and is the first such study to be performed on microorganisms growing in epilithic biofilms and microbial mats along the coastline in the Maltese islands. Samples were obtained using techniques that were noninvasive to the underlying substratum. These were studied by direct observation using light and electron microscopy, by culturing in vitro, by molecular analysis via sequencing of the small subunit ribosomal ribonucleic acid genes and phylogenetic analyses. Microscopic analyses revealed highly diverse communities made of both photosynthetic and heterotrophic organisms. The predominant microorganisms were simple filamentous cyanobacteria including species of Leptolyngbya, Phormidesmis, Nodosilinea, Toxifilum, Phormidium, and Lyngbya, as well as heterocytous Calothrix and Nunduva spp. The coccal cyanobacteria included species of Aphanocapsa and Chroococcus, whereas coccal microalgae belonged to Chlorella, Chlamydomonas, and Coelastrella spp., accompanied by diatoms of Navicula sp. These results include first records of cyanobacterial and microalgal barcodes that were genetically sequenced from a coastline in the central Mediterranean. Germlings of the filamentous macroalga Cladophora were embedded in the rocky substrate that was preconditioned by biofilm growth and ciliated protozoans, micronematodes, and microcrustaceans interacted with the microbial communities. The isolation of new cyanobacterial and microalgal strains from these phototrophic communities highlights the importance of employing a combined multiphasic approach to supplement current knowledge about the biodiversity of microbial communities colonising rocky shores.

Many show caves are vulnerable to various disturbances, meaning that conservation of such habitats, which would include monitoring of their ecological parameters and lampenflora (a growing problem worldwide), should be a priority. For the first time in Serbia, lampenflora was monitored continously for 5 years (2016–2020), three times per year during the tourist season, in the Lazar Cave. Artificial light created favorable conditions for the proliferation of phototrophic microorganisms that were developed not only as epiliths, but also endoliths, which poses a greater danger for cave substratum and structures. Although a higher diversity in general was found in Cyanobacteria (coccoid forms mostly), Chlorophyta were more widespread and abundant in samples, among which Chlorella , Stichococcus bacillaris , and Klebsormidium flaccidum stood out. Chlorella is one of the genera making lampenflora dangerous, as it can switch from an autotrophic to a mixotrophic, and finally to a heterotrophic lifestyle. The mosses protonema and mosses itself were also present. Even though the cave is closed for 6 months every year, lampenflora “legacy” always persisted on all sites from the previous year, spreading further over the years. Measured parameters (temperature, relative air humidity, light intensity, substrate pH, and substratum moisture), primary production, and biofilm parameters showed yearly, seasonal, or sampling site variations. Statistical analyses were used to examine the effect of the sampling year, the season, and sampling site on the selected measured parameters, while multivariate analyses were performed with taxa in relation to year, season, site, and main ecological parameters.

Phototrophic microbial communities present in the Roman Catacombs were characterized and different species of terrestrial epilithic cyanobacteria were found to occur as dominant organisms. Eucapsis, Leptolyngbya, Scytonema, and Fischerella were the most frequently encountered cyanobacterial taxa, while a few species of green algae and the diatom Diadesmis gallica occurred in minor amounts. Streptomyces strains, a few genera of eubacteria, and to a lesser extent fungi were always present in the same microhabitats and contributed to the deterioration of stone surfaces. The combined use of light and electron microscopy evidenced the structural relationships among rodshaped or filamentous bacteria and cyanobacterial cells, as well as the presence of polysaccharide capsules and sheaths, and of mineral precipitates on S. julianum filaments. The significance of the intimate association among the microorganisms was discussed in relation to the damage caused by the growth of biological patinas on stone surfaces.

Disturbances to forested watersheds often result in increases of nutrients and light to nearby streams. Such changes are generally expected to produce a shift to a more autotrophic aquatic ecosystem, with measurable increases in algae, and associated implications for food webs and fisheries. Although this paradigm is widely established, results from our 10-year study (2007–2016) in 12 headwater streams and four sites downstream in the Trask River Watershed (Oregon, USA), did not concur. In 2012, one watershed was thinned, three were clearcut harvested with variable buffers and three with uniform riparian buffers. After harvest, light to the stream surface significantly increased at the three watersheds with variable buffers while dissolved inorganic nitrogen (DIN) significantly increased in all of the clearcut harvested streams. Despite the increase in DIN and light, algal standing stocks and chlorophyll a concentrations did not significantly increase. The common assumption of increased autotrophic responses in stream food webs following increases of nitrogen and light was not supported here. We postulate the co-limitation of nutrients, driven by low phosphorus concentrations, which unlike DIN did not increase post-harvest, and the characteristics of the algal community, which were dominated by low light adapted diatoms rather than green algae, contributed to our findings of no responses for standing stocks of epilithic algae or concentrations of chlorophyll a . The inclusion of multiple statistical analyses provided more certainty around our findings. This study documents responses to current forest practices and provides cautionary information for management and restoration activities aiming to increase fish abundance and standing stocks by opening riparian canopies and adding nutrients.

Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification–denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA , hao , and nxrB involved in nitrification, and napA , narG , nirS , norB , and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon–nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB . As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria , substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis . Considering the genes’ functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.

Macroalgal competition can indirectly influence the health of corals and their response to changing environmental conditions by altering their associated bacterial community. However, the effect of macroalgae on the composition of epilithic microbial biofilms, an important determinant of coral recruitment, is poorly known. In the back-reefs of Moorea (French Polynesia), we evaluated how the experimental removal of either the canopy of the seaweed Turbinaria ornata or that of the entire macroalgal assemblage influenced the composition of the bacterial biofilm and coral recruitment on macroalga-free substrata. The number of bacterial colonies on culture plates inoculated with dilutions of 9 d old biofilm from canopy removal sites was smaller compared with control sites. After 3.5 mo, the diversity of bacterial operational taxonomic units (OTUs) was lower at both canopy and total macroalgal removal sites. Total macroalgal removal sites had a lower relative abundance of several bacterial families, including Rhodobacteraceae, Erythrobacteraceae, Cyanobacteria Family IV and Family VIII, Flavobacteriaceae and Verrucomicrobiaceae. After 8 mo, coral recruitment was generally low, but greater at total macroalgal removal sites. The relative abundance of Cyanobacteria, Sphingobacteria and Verrucomicrobia was negatively correlated with coral recruitment and explained ~70% of variation in coral recruit density. Our study shows that the removal of T. ornata and understory macroalgae influences the composition of epilithic bacterial assemblages and coral recruitment. Thus, eradication campaigns are unlikely to sustain long-term reductions in the abundance of T. ornata and, hence, increase coral recruitment, when plant holdfasts and understory macroalgae are left in place.

The aim of this study is to determine the epilithic diatom flora of stations exposed to pollutants of different characteristics, to test the relationships of these diatoms with water quality and the suitability of environmental quality indicators, and to determine different indicators of various quality pollutants for the rapid assessment of ecological pollution. Additionally, determining the ecological impact of both industrial and domestic waste on the reservoir in the region and determining whether the diatom community changes when exposed to various pollutants (including potential mortality), especially its role as an indicator of metal pollution; Samples taken from stations where domestic and industrial wastes were discharged with different chemical properties were evaluated and investigated. A total of 100 species were identified for Bacillariophyta. Although there was no significant change in the number of the species among the stations, significant changes were observed in the community structure. While Achnanthidium minutissimum, Fragilaria capucina, Gomphonema parvulum, Nitzschia palea and Surirella angustatum were the dominant diatoms in the impermeable artificial pool where the industrial wastewater of the factory was collected, Nitzschia amphibia, N. palea, N. recta and Ulnaria ulna were the dominant diatoms of the station where domestic wastewater was discharged. In the dam area where domestic wastewater is discharged, Fragilaria capucina Ulnaria ulna and Diatoma vulgaris are the dominant diatoms. Achnanthidium minutissimum, Gomphonema parvulum Navicula cinta and Nitzschia amphibia, N. angustata were the dominant diatoms of the station where both domestic and industrial wastewater was discharged. It was determined that benthic diatoms responded to different types of waste by changing their species composition, and that the change in the benthic community was not due to seasonal differences in stations under the influence of pollutants with different chemical properties. Diatom taxa which are known to tolerate metal concentrations, diatom diversities, and teratologies were determined.

Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.

Temperate rocky reefs often support mosaics of alternative habitats such as macroalgal forests, algal turfs and sea urchin barrens. Although the composition of epilithic microbial biofilms (EMBs) is recognized as a major determinant of macroalgal recruitment, their role in regulating the stability of alternative habitats on temperate rocky reefs remains unexplored. On shallow rocky reefs of the Island of Capraia (NW Mediterranean), we compared EMB structure among canopy stands formed by the fucoid Ericaria brachycarpa , algal turfs, and urchin barrens under ambient versus experimentally enhanced nutrient levels. The three habitats shared a core microbial community consisting of 21.6 and 25.3% of total ASVs under ambient and enhanced nutrient conditions, respectively. Although Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia were the most abundant classes across habitats, multivariate analyses at the ASV level showed marked differences in EMB composition among habitats. Enhancing nutrient level had no significant effect on EMBs, although it increased their similarity between macroalgal canopy and turf habitats. At both ambient and enriched nutrient levels, ASVs mostly belonging to Proteobacteria and Bacteroidetes were more abundant in EMBs from macroalgal canopies than barrens. In contrast, ASVs belonging to the phylum of Proteobacteria and, in particular, to the families of Rhodobacteraceae and Flavobacteriaceae at ambient nutrient levels and of Rhodobacteraceae and Bacteriovoracaceae at enhanced nutrient levels were more abundant in turf than canopy habitats. Our results show that primary surfaces from alternative habitats that form mosaics on shallow rocky reefs in oligotrophic areas host distinct microbial communities that are, to some extent, resistant to moderate nutrient enhancement. Understanding the role of EMBs in generating reinforcing feedback under different nutrient loading regimes appears crucial to advance our understanding of the mechanisms underpinning the stability of habitats alternative to macroalgal forests as well as their role in regulating reverse shifts.