Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances.

BACKGROUND: Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances. RESULTS: The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions. CONCLUSIONS: Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes.

The spatial distribution and biogeochemical drivers of nitrogen cycle genes in an Antarctic desert.

Antarctic deserts, such as the McMurdo Dry Valleys (MDV), represent extremely cold and dry environments. Consequently, MDV are suitable for studying the environment limits on the cycling of key elements that are necessary for life, like nitrogen. The spatial distribution and biogeochemical drivers of nitrogen-cycling pathways remain elusive in the Antarctic deserts because most studies focus on specific nitrogen-cycling genes and/or organisms. In this study, we analyzed metagenome and relevant environmental data of 32 MDV soils to generate a complete picture of the nitrogen-cycling potential in MDV microbial communities and advance our knowledge of the complexity and distribution of nitrogen biogeochemistry in these harsh environments. We found evidence of nitrogen-cycling genes potentially capable of fully oxidizing and reducing molecular nitrogen, despite the inhospitable conditions of MDV. Strong positive correlations were identified between genes involved in nitrogen cycling. Clear relationships between nitrogen-cycling pathways and environmental parameters also indicate abiotic and biotic variables, like pH, water availability, and biological complexity that collectively impose limits on the distribution of nitrogen-cycling genes. Accordingly, the spatial distribution of nitrogen-cycling genes was more concentrated near the lakes and glaciers. Association rules revealed non-linear correlations between complex combinations of environmental variables and nitrogen-cycling genes. Association rules for the presence of denitrification genes presented a distinct combination of environmental variables from the remaining nitrogen-cycling genes. This study contributes to an integrative picture of the nitrogen-cycling potential in MDV.

Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica.

Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific.

Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3 -). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3 - concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.

Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods.

Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families: Sporichthyaceae, Euzebyaceae, Patulibacteraceae, Nocardioidaceae, and Rubrobacteraceae. However, the 11 actinobacterial strains isolated in this study, belonged to Micrococcaceae and Dermacoccaceae families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (Nodosilinea, Leptolyngbya, Pectolyngbya, and Acaryochloris-like). In agreement with the cultivation results, Leptolyngbya was identified as dominant genus in the HTS data set. Acaryochloris-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this Acaryochloris-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.

Impacts of Silver Nanoparticles on a Natural Estuarine Plankton Community.

Potential effects of metal nanoparticles on aquatic organisms and food webs are hard to predict from the results of single-species tests under controlled laboratory conditions, and more realistic exposure experiments are rarely conducted. We tested whether silver nanoparticles (Ag NPs) had an impact on zooplankton grazing on their prey, specifically phytoplankton and bacterioplankton populations. If Ag NPs directly reduced the abundance of prey, thereby causing the overall rate of grazing by their predators to decrease, a cascading effect on a planktonic estuarine food web would be seen. Our results show that the growth rates of both phytoplankton and bacterioplankton populations were significantly reduced by Ag NPs at concentrations of ≥500 µg L(-1). At the same time, grazing rates on these populations tended to decline with exposure to Ag NPs. Therefore, Ag NPs did not cause a cascade of effects through the food web but impacted a specific trophic level. Photosynthetic efficiency of the phytoplankton was significantly reduced at Ag NPs concentrations of ≥500 µg L(-1). These effects did not occur at relatively low concentrations of Ag that are often toxic to single species of bacteria and other organisms, suggesting that the impacts of Ag NP exposure may not be apparent at environmentally relevant concentrations due to compensatory processes at the community level.

Assessment of the non-protein amino acid BMAA in Mediterranean mussel Mytilus galloprovincialis after feeding with estuarine cyanobacteria.

To determine whether 2-amino-3-methylaminopropanoic acid (BMAA) could be taken up by marine organisms from seawater or their diet mussels Mytilus galloprovincialis, collected from the North Atlantic Portuguese shore, were exposed to seawater doped with BMAA standard (for up to 48 h) or fed with cyanobacteria (for up to 15 days). Mussels were able to uptake BMAA when exposed to seawater. Mussels fed with cyanobacteria Synechocystis salina showed a rise in BMAA concentration during feeding and a decline in concentration during the subsequent depuration period. Cells from the gills and hepatopancreas of mussels fed with S. salina showed lessened metabolic activity in mussels fed for longer periods of time. A hot acidic digestion (considered to account for total BMAA) was compared with a proteolytic digestion, using pepsin, trypsin and chymotrypsin. The latter was able to extract from mussels approximately 30% of total BMAA. Implications for BMAA trophic transfers in marine ecosystems are discussed.

Trace metal concentration in a temperate freshwater reservoir seasonally subjected to blooms of toxin-producing cyanobacteria.

In situ interactions between cyanobacteria and metals were studied at Torrão reservoir (Tâmega River, North Portugal). The metal content of water and sediments from the reservoir was monitored monthly at Marco de Canaveses (seasonally subjected to toxic blooms of Microcystis aeruginosa) and upstream at Amarante (no blooms recorded), for 16 months. During the 16 months of the study period, M. aeruginosa bloomed twice at Marco de Canaveses, firstly forming a scum, and later with colonies scattered throughout the reservoir. Metals Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn were analysed in the sediment and in the water column. Cu-binding ligands in water were also determined. When no blooms were taking place, average metal levels for water and sediment were not statistically different at both locations. Therefore, it was considered that the absence of cyanobacteria blooms at Amarante was not due to differences in metal content. When blooms were taking place at Marco de Canaveses, a significant increase of metal levels in the sediment occurred simultaneously. Sediment quality guidelines showed that during this period, Cu and Pb concentrations (32.3 and 43.2 mg kg(-1), respectively) were potentially toxic. However, quantification of the exchangeable metal fraction indicated that these metals were probably not bioavailable. Concentration of Cu-binding ligands in water was higher during the blooms, indicating that cyanobacteria are capable of changing the metal speciation in situ in a reservoir.

The non-protein amino acid ß-N-methylamino-L-alanine in Portuguese cyanobacterial isolates.

The tailor made amino acid ß-N-methyl-amino-L-alanine (BMAA) is a neurotoxin produced by cyanobacteria. It has been associated with certain forms of progressive neurodegenerative disease, including sporadic Amyotrophic Lateral Sclerosis and Alzheimer's disease. Some different reports of BMAA in cyanobacterial blooms from lakes, reservoirs, and other water resources have been made by different investigators. We here report the detection of BMAA of both free and protein-bound produced by cyanobacteria, belonging to the Chroococcales, Oscillatoriales and Nostocales ordered. We use a rapid and sensitive HPLC-FD method that utilizes methanol elution and the Waters AQC Tag chemistry. On other hand, we have used three different assay procedures for BMAA extraction from cyanobacteria: Trichloroacetic acid (TCA), Methanol/Acetone and hydrochloric acid (HCl). All assays let successfully detect BMAA in all cyanobacteria samples analyzed. Nevertheless, with TCA and HCl extraction procedures the highest BMAA values, for free as well as protein-bound BMAA were detected. BMAA content could not be related to the taxonomy of the isolates or to their geographical origin, and no correlation between free and protein-bound BMAA concentrations were observed within or between taxonomic groups. These data offer confirmation of the taxonomic and geographic ubiquity of BMAA from naturally occurring populations of cyanobacteria, for the first time reported for estuaries.

Determination of the non protein amino acid ß-N-methylamino-l-alanine in estuarine cyanobacteria by capillary electrophoresis.

A capillary electrophoretic method for the determination of the amino acid ß-N-methylamino-l-alanine (BMAA) was achieved using a fused-silica capillary column (50 cm × 75 µm I.D.) filled with 5 mM sodium tetraborate solution (pH 9), with an applied voltage of 25 kV, at 25 °C. The method was then applied in quantifying BMAA in eighteen strains of lyophilized estuarine cyanobacteria, following amino acid extraction using 0.1 M trichloroacetic acid and 6 M hydrochloric acid, sequentially.

Effects of minocycline and its degradation products on the growth of Microcystis aeruginosa.

This work aimed to investigate the influence of Microcystis aeruginosa on the rate of minocycline (MNC) removal (abiotic degradation, physical binding or chemical transformation by cells) and the toxicity of MNC and its degradation products to the cyanobacterium. Most of the work was carried out in culture media in the presence or in the absence of M. aeruginosa. The rate of the MNC abiotic degradation in culture media strongly decreased with the increase of the MNC initial concentration. The exudates did not influence the rate of MNC degradation in the media. For concentrations ≥0.48 µM, the rate of the MNC removal from the media was faster in the presence of M. aeruginosa. Biotic MNC removal occurs by both physical binding by the cells (10%) and chemical transformations. EC(50) and EC(20) for MNC on the growth of M. aeruginosa were 0.92 and 0.13 µM, respectively. Interestingly, MNC degradation products might promote M. aeruginosa growth.

Fate and effects of octylphenol in a Microcystis aeruginosa culture medium.

Octylphenol (OP) is a xenobiotic with endocrine disrupting properties found in freshwaters worldwide. Its effects have been studied in organisms with nuclear receptors but effects on phytoplankton communities are poorly characterized, despite the fact that these organisms are constantly exposed to this compound. For this reason fate and effects of OP in the cyanobacterium Microcystis aeruginosa were assessed from 10 nM to 5 microM OP concentration. Up to a test concentration of 250 nM, OP removal increased significantly in the presence of cyanobacteria, the compound half-life in the absence of cells being 15 days against 9 days in the presence of the cells. Only 4% of the total OP removed was found bound to the cells, indicating an active metabolization of the compound. Moreover, the role of the exudates produced by M. aeruginosa, in the OP removal from culture medium, was assessed. Culture medium with exudates, resulting from a 7-day growth of M. aeruginosa, spiked with 50 nM OP, showed a higher half-life (22 days). Compared to culture medium without exudates, it can be hypothesized that higher organic matter concentrations make the hydrolysis or photolysis of OP more difficult. In culture media, the cells of M. aeruginosa could compensate and even counteract this, as OP half-life was shortened. At higher OP levels (1.25 and 5 microM) M. aeruginosa growth was impaired, indicating toxic effects. This shortage of biomass prevented the M. aeruginosa-assisted OP withdrawal from the culture media.

Application of SPME to the determination of alkylphenols and bisphenol A in cyanobacteria culture media.

In order to survey the influence of estrogenic compounds on cyanobacteria, solid-phase microextraction (SPME) with a carbowax-divinylbenzene fibre was used for the determination of tert-octylphenol (tert-OP), n-nonylphenol (n-NP), technical nonylphenol (tech-NP) and bisphenol A (BPA) in cyanobacteria culture media by gas chromatography with flame ionization detection. Determinations were carried out without derivatization in deionized water and filtered culture media. A comparison between f2 and Fraquil culture media was performed, which showed that only f2 allowed quantitative recoveries. Headspace SPME with salting out, requiring only 10 mL of sample, was suitable for tert-OP, n-NP, and tech-NP determination with limits of detection (LOD) of <0.05 microg L(-1). For BPA, direct immersion SPME could provide a LOD of 1 microg L(-1). Automated sampling allowed reproducible extraction. No exudate substances overlapped with the studied compounds during the chromatographic separation and no matrix effects were observed. Ecotoxicity tests can be performed by single spiking of tert-OP and tech-NP and multiple spiking of n-NP due to its lower stability.

Copper, nickel and lead in lichen and tree bark transplants over different periods of time.

This work aimed at comparing the dynamics of atmospheric metal accumulation by the lichen Flavoparmelia caperata and bark of Platanus hybrida over different periods of time. Transplants were exposed in three Portuguese coastal cities. Samples were retrieved (1) every 2 months (discontinuous exposure), or (2) after 2-, 4-, 6-, 8- and 10-month periods (continuous exposure), and analysed for Cu, Ni and Pb. Airborne accumulation of metals was essentially independent of climatic factors. For both biomonitors [Pb]>[Ni]>[Cu] but Pb was the only element for which a consistent pattern of accumulation was observed, with the bark outperforming the lichen. The longest exposure periods hardly ever corresponded to the highest accumulation. This might have been partly because the biomonitors bound and released metals throughout the exposure, each with its own dynamics of accumulation, but both according to the environmental metal availability.

Cyanobacteria metal interactions: requirements, toxicity, and ecological implications.

The environmental health-related relevance of cyanobacteria is primarily related to their ability to produce a wide range of toxins, which are known to be hazardous to many organisms, including human beings. The occurrence of cyanobacterial blooms has been related to eutrophic surface water. In the bloom-forming process the levels of phosphorus and nitrogen have been well documented but information regarding concentrations of other chemicals (inorganic, organo-metallic, and organic) is still incipient. Several contaminants, like trace metals, elicit a variety of acute and chronic toxicity effects, but cyanobacteria also have the capability to accumulate, detoxify, or metabolize such substances, to some extent. The role of cyanobacterial exudates has been proved a means of both nutrient acquisition and detoxification. In addition, cyanobacteria are effective biological metal sorbents, representing an important sink for metals in aquatic environment. Understanding the fundamental physicochemical mechanisms of trace metal bio-uptake by cyanobacteria in natural systems is a step towards identifying under what conditions cyanobacterial growth is favored and to ascertain the mechanisms by which blooms (and toxin production) are triggered. In this review the cyanobacterial interactions with metals will be discussed, focusing on freshwater systems.

The ability of biological and organic synthetic materials to accumulate atmospheric particulates containing copper, lead, nickel and strontium.

This work was aimed at finding materials that could be used as alternatives to lichens as air quality monitors since the high natural variability and the large amount of lichen collected are two drawbacks of the use of these organisms. Lichen Flavoparmelia caperata(L.) Hale was exposed in three different forms (transplant, detached from the substratum and as a biomass-ground and homogeneized) and compared to the planetree bark (Platanus hybrida Brot.), exposed as a biomass, and two organic synthetic materials (Chelex(R) 100 resin and cellulose acetate). Materials were exposed for two months in the winter, spring and summer, at three Portuguese coastal cities. The results showed that the airborne accumulations of Cu, Ni, Pb and Sr were partially dependent on the meteorological conditions but mainly dependent on the nature of the exposed material. The standard deviations of the synthetic materials or homogenized biomass were the same or greater than lichen transplants or detached. The accumulation by biological materials, of the four studied elements, was comparable to the lichen transplant accumulation. The replacement of the traditional transplants by the biomass was not considered advantageous, since their preparation is time-consuming. Therefore lichens remain the most suitable in biomonitoring studies. The exposure of detached lichen allows the accurate measurement of the exposed area/volume so it can be useful to relate atmospheric deposition rates with the lichen metal content. The synthetic materials accumulated Cu and Ni and should only be used as an alternative to traditional transplants when these are the elements of interest.