Protist communities of microbial mats from the extreme environments of five saline Andean lagoons at high altitudes in the Atacama Desert.

Introduction: Heterotrophic protists colonizing microbial mats have received little attention over the last few years, despite their importance in microbial food webs. A significant challenge originates from the fact that many protists remain uncultivable and their functions remain poorly understood. Methods: Metabarcoding studies of protists in microbial mats across high-altitude lagoons of different salinities (4.3-34 practical salinity units) were carried out to provide insights into their vertical stratification at the millimeter scale. DNA and cDNA were analyzed for selected stations. Results: Sequence variants classified as the amoeboid rhizarian Rhogostoma and the ciliate Euplotes were found to be common members of the heterotrophic protist communities. They were accompanied by diatoms and kinetoplastids. Correlation analyses point to the salinity of the water column as a main driver influencing the structure of the protist communities at the five studied microbial mats. The active part of the protist communities was detected to be higher at lower salinities (<20 practical salinity units). Discussion: We found a restricted overlap of the protist community between the different microbial mats indicating the uniqueness of these different aquatic habitats. On the other hand, the dominating genotypes present in metabarcoding were similar and could be isolated and sequenced in comparative studies (Rhogostoma, Euplotes, Neobodo). Our results provide a snapshot of the unculturable protist diversity thriving the benthic zone of five athalossohaline lagoons across the Andean plateau.

Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland.

Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community.

Shared governance in the plant holobiont and implications for one health.

The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.

Exploring the potential of the halotolerant bacterial strain Bacillus subtilis LN8B as an ecofriendly sulfide collector for seawater flotation.

AIM: To assess the effectiveness of Bacillus subtilis strain LN8B as a biocollector for recovering pyrite (Py) and chalcopyrite (CPy) in both seawater (Sw) and deionized water (Dw), and to explore the underlying adhesion mechanism in these bioflotation experiments. MATERIALS AND METHODS: The bioflotation test utilized B. subtilis strain LN8B as the biocollector through microflotation experiments. Additionally, frother methyl isobutyl carbinol (MIBC) and conventional collector potassium amyl xanthate (PAX) were introduced in some experiments. The zeta potential (ZP) and Fourier-transform infrared spectroscopy (FTIR) was employed to explore the adhesion mechanism of Py and CPy interacting with the biocollector in Sw and Dw. The adaptability of the B. subtilis strain to different water types and salinities was assessed through growth curves measuring optical density. Finally, antibiotic susceptibility tests were conducted to evaluate potential risks of the biocollector. RESULTS: Superior outcomes were observed in Sw where Py and CPy recovery was ∼39.3% ± 7.7% and 41.1% ± 5.8%, respectively, without microorganisms' presence. However, B. subtilis LN8B potentiate Py and CPy recovery, reaching 72.8% ± 4.9% and 84.6% ± 1.5%, respectively. When MIBC was added, only the Py recovery was improved (89.4% ± 3.6%), depicting an adverse effect for CPy (81.8% ± 1.1%). ZP measurements indicated increased mineral surface hydrophobicity when Py and CPy interacted with the biocollector in both Sw and Dw. FTIR revealed the presence of protein-related amide peaks, highlighting the hydrophobic nature of the bacterium. The adaptability of this strain to diverse water types and salinities was assessed, demonstrating remarkable growth versatility. Antibiotic susceptibility tests indicated that B. subtilis LN8B was susceptible to 23 of the 25 antibiotics examined, suggesting it poses minimal environmental risks. CONCLUSIONS: The study substantiates the biotechnological promise of B. subtilis strain LN8B as an efficient sulfide collector for promoting cleaner mineral production. This effectiveness is attributed to its ability to induce mineral surface hydrophobicity, a result of the distinct characteristics of proteins within its cell wall.

Gregarines from darkling beetles of the Atacama Desert, Atacamagregarina paposa gen. et sp. nov. from Scotobius and Xiphocephalus ovatus sp. nov. from Psectrascelis (Coleoptera, Tenebrionidae).

Gregarine apicomplexans, a group of single celled organisms, inhabit the extracellular spaces of most invertebrate species. The nature of the gregarine-host interactions is not yet fully resolved, mutualistic, commensal and parasitic life forms have been recorded. In the extreme arid environment of the Atacama Desert, only a few groups of invertebrates hosting gregarines such as darkling beetles (Tenebrionidae) were able to adapt, providing an unparalleled opportunity to study co-evolutionary diversification. Here, we describe one novel gregarine genus comprising one species, Atacamagregarina paposa gen. et sp. nov., and a new species, Xiphocephalus ovatus sp. nov. (Apicomplexa: Eugregarinoridea, Stylocephalidae), found in the tenebrionid beetle genera Scotobius (Tenebrioninae, Scotobiini) and Psectrascelis intricaticollis ovata (Pimeliinae, Nycteliini), respectively. In the phylogenetic analysis based on SSU rDNA, Atacamgregarina paposa representing the new genus is basal, forming a separate clade with terrestrial gregarines specific for North American darkling beetles.

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis.

At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

The microbial world in copper sulfide flotation plants (CSFP): Novel insights into bacterial communities and their application as potential pyrite bioreagents.

Operations in copper sulfide flotation plants (CSFP) are complex and governed by several variables such as available technologies, reagents, and environmental conditions. However, few investigations are related to studying the microbial communities. These aspects provide a reason to compare the bacterial communities of two CSFP operated with freshwater (FwFlo) and seawater (SwFlo), and study whether indigenous bacteria could be used as pyrite bioreagents. Analyses were determined through next-generation sequencing by Illumina MiSeq System and conducted throughout the entire process: (i) minerals before and after grinding; (ii) final concentrate and concentrate thickener overflow; (iii) final tailings and tailings thickener overflow; and (iv) intake water. Bacterial strains from both plants were tested as potential bioreagents, given their tendency to adhere to pyrite after 5 min. In both CSFP, Proteobacteria (relative abundance from 45.48% to 79.22%), followed by Bacteroidetes (9.37%-44.7%), were the most abundant phyla. Regarding species, Algoriphagus olei (11.35%-43.52%) was present exclusively in FwFlo samples in contact with process water and absent in the mineral before grinding, where Cupriavidus metallidurans (16.05%) and Pseudomonas_uc (11.79%) predominated. In SwFlo samples, Marinobacter flavimaris (3.47%-41.1%), and GU061212-s (10.92%-27.63%), were the most abundant microorganisms. All of them were also detected in intake seawater. The strains with the highest adhesion rate (from 29.84% ± 0.14-100%) were phylogenetically identified as species of the genera Marinobacter, Pseudomonas, Idiomarina, Halomonas, Bacillus, Aerocuccus, and Peribacillus. Our results reveal that bacterial communities are critically dependent on process waters during mining activities, and our data depicted that indigenous bacteria could be used as potential pyrite bioreagents, evidenced by a high adhesion rate. It is thus possible to propose that different indigenous bacterial strains could be considered as new bioreagents to reduce the impact of conventional flotation reagents on health from an environment friendly perspective.

Virus-to-prokaryote ratio in the Salar de Huasco and different ecosystems of the Southern hemisphere and its relationship with physicochemical and biological parameters.

The virus-to-prokaryote ratio (VPR) has been used in many ecosystems to study the relationship between viruses and their hosts. While high VPR values indicate a high rate of prokaryotes' cell lysis, low values are interpreted as a decrease in or absence of viral activity. Salar de Huasco is a high-altitude wetland characterized by a rich microbial diversity associated with aquatic sites like springs, ponds, streams and a lagoon with variable physicochemical conditions. Samples from two ponds, Poza Rosada (PR) and Poza Verde (PV), were analyzed by epifluorescence microscopy to determine variability of viral and prokaryotic abundance and to calculate the VPR in a dry season. In addition, to put Salar de Huasco results into perspective, a compilation of research articles on viral and prokaryotic abundance, VPR, and metadata from various Southern hemisphere ecosystems was revised. The ecosystems were grouped into six categories: high-altitude wetlands, Pacific, Atlantic, Indian, and Southern Oceans and Antarctic lakes. Salar de Huasco ponds recorded similar VPR values (an average of 7.4 and 1.7 at PR and PV, respectively), ranging from 3.22 to 15.99 in PR. The VPR variability was associated with VA and chlorophyll a, when considering all data available for this ecosystem. In general, high-altitude wetlands recorded the highest VPR average (53.22 ± 95.09), followed by the Oceans, Southern (21.91 ± 25.72), Atlantic (19.57 ± 15.77) and Indian (13.43 ± 16.12), then Antarctic lakes (11.37 ± 15.82) and the Pacific Ocean (6.34 ± 3.79). Physicochemical variables, i.e., temperature, conductivity, nutrients (nitrate, ammonium, and phosphate) and chlorophyll a as a biological variable, were found to drive the VPR in the ecosystems analyzed. Thus, the viral activity in the Wetland followed similar trends of previous reports based on larger sets of metadata analyses. In total, this study highlights the importance of including viruses as a biological variable to study microbial temporal dynamics in wetlands considering their crucial role in the carbon budgets of these understudied ecosystems in the southern hemisphere.

A mechanistic understanding of polyethylene biodegradation by the marine bacterium Alcanivorax.

Polyethylene (PE) is one of the most recalcitrant carbon-based synthetic materials produced and, currently, the most ubiquitous plastic pollutant found in nature. Over time, combined abiotic and biotic processes are thought to eventually breakdown PE. Despite limited evidence of biological PE degradation and speculation that hydrocarbon-degrading bacteria found within the plastisphere is an indication of biodegradation, there is no clear mechanistic understanding of the process. Here, using high-throughput proteomics, we investigated the molecular processes that take place in the hydrocarbon-degrading marine bacterium Alcanivorax sp. 24 when grown in the presence of low density PE (LDPE). As well as efficiently utilising and assimilating the leachate of weathered LDPE, the bacterium was able to reduce the molecular weight distribution (Mw from 122 to 83 kg/mol) and overall mass of pristine LDPE films (0.9 % after 34 days of incubation). Most interestingly, Alcanivorax acquired the isotopic signature of the pristine plastic and induced an extensive array of metabolic pathways for aliphatic compound degradation. Presumably, the primary biodegradation of LDPE by Alcanivorax sp. 24 is possible via the production of extracellular reactive oxygen species as observed both by the material's surface oxidation and the measurement of superoxide in the culture with LDPE. Our findings confirm that hydrocarbon-biodegrading bacteria within the plastisphere may in fact have a role in degrading PE.

The metabolite p-cresol impairs dendritic development, synaptogenesis, and synapse function in hippocampal neurons: Implications for autism spectrum disorder.

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopment disorder resulting from different etiological factors, both genetic and/or environmental. These factors can lead to abnormal neuronal development on dendrite and synaptic function at the central nervous system. Recent studies have shown that a subset of ASD patients display increased circulation levels of the tyrosine metabolite, p-cresol, related to chronic intestinal disorders because of dysbiosis of the intestinal microbiota. In particular, abnormal presence of intestinal Clostridium sp. has been linked to high levels of p-cresol in ASD children younger than 8 years. However, the role of p-cresol during development of the central nervous system is unknown. Here, we evaluated in vitro the effect of p-cresol on neurite outgrowth in N2a and PC12 cell lines and dendritic morphology, synaptic density, neuronal activity, and calcium responses in primary rat hippocampal neurons. p-cresol inhibits neural differentiation and neurites outgrowth in N2a and PC12 neuronal cell lines. In hippocampal neuronal cultures, Sholl's analysis shows a decrease in the dendritic arborization of neurons treated with p-cresol. Synaptic density analyzed with the synaptic markers Piccolo and Shank2 is diminished in hippocampal neurons treated with p-cresol. Electrically evoked intracellular calcium rise was drastically, but reversely, blocked by p-cresol, whereas that spontaneous neuronal activity was severely affected by early addition of the metabolite. These findings show that p-cresol alters dendrite development, synaptogenesis, and synapse function of neurons in culture, therefore, neuronal alterations occurring in ASD children may be related to this metabolite and dysbiosis of the intestinal microbiota.

Climate change and lithium mining influence flamingo abundance in the Lithium Triangle.

The development of technologies to slow climate change has been identified as a global imperative. Nonetheless, such 'green' technologies can potentially have negative impacts on biodiversity. We explored how climate change and the mining of lithium for green technologies influence surface water availability, primary productivity and the abundance of three threatened and economically important flamingo species in the 'Lithium Triangle' of the Chilean Andes. We combined climate and primary productivity data with remotely sensed measures of surface water levels and a 30-year dataset on flamingo abundance using structural equation modelling. We found that, regionally, flamingo abundance fluctuated dramatically from year-to-year in response to variation in surface water levels and primary productivity but did not exhibit any temporal trends. Locally, in the Salar de Atacama-where lithium mining is focused-we found that mining was negatively correlated with the abundance of two of the three flamingo species. These results suggest continued increases in lithium mining and declines in surface water could soon have dramatic effects on flamingo abundance across their range. Efforts to slow the expansion of mining and the impacts of climate change are, therefore, urgently needed to benefit local biodiversity and the local human economy that depends on it.

Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco.

The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.

Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline.

Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.

Micromonospora tarapacensis sp. nov., a bacterium isolated from a hypersaline lake.

Strain Llam7T was isolated from microbial mat samples from the hypersaline lake Salar de Llamará, located in Taracapá region in the hyper-arid core of the Atacama Desert (Chile). Phenotypic, chemotaxonomic and genomic traits were studied. Phylogenetic analyses based on 16S rRNA gene sequences assigned the strain to the family Micromonosporaceae with affiliation to the genera Micromonospora and Salinispora. Major fatty acids were C17 : 1ω8c, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The cell walls contained meso-diaminopimelic acid and ll-2,6 diaminopimelic acid (ll-DAP), while major whole-cell sugars were glucose, mannose, xylose and ribose. The major menaquinones were MK-9(H4) and MK-9(H6). As polar lipids phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and several unidentified lipids, i.e. two glycolipids, one aminolipid, three phospholipids, one aminoglycolipid and one phosphoglycolipid, were detected. Genome sequencing revealed a genome size of 6.894 Mb and a DNA G+C content of 71.4 mol%. Phylogenetic analyses with complete genome sequences positioned strain Llam7T within the family Micromonosporaceae forming a distinct cluster with Micromonospora (former Xiangella) phaseoli DSM 45730T. This cluster is related to Micromonospora pelagivivens KJ-029T, Micromonospora craterilacus NA12T, and Micromonospora craniellae LHW63014T as well as to all members of the former genera Verrucosispora and Jishengella, which were re-classified as members of the genus Micromonospora, forming a clade distinct from the genus Salinispora. Pairwise whole genome average nucleotide identity (ANI) values, digital DNA-DNA hybridization (dDDH) values, the presence of the diamino acid ll-DAP, and the composition of whole sugars and polar lipids indicate that Llam7T represents a novel species, for which the name Micromonospora tarapacensis sp. nov. is proposed, with Llam7T (=DSM 109510T,=LMG 31023T) as the type strain.

Benthic microbial diversity trends in response to heavy metals in an oxygen-deficient eutrophic bay of the Humboldt current system offshore the Atacama Desert.

Mejillones Bay is a coastal ecosystem situated in an oxygen-deficient upwelling area impacted by mining activities in the coastal desert region of northern Chile, where conspicuous microbial life develops in the sediments. Herein, heavy metal (loid)s (HMs) such as Cu, Pb, As, Zn, Al, Fe, Cd, Mo, Ni and V as well as benthic microbial communities were studied using spectrometry and iTag-16 S rRNA sequencing. Samples were taken from two contrasting sedimentary localities in the Bay named Punta Rieles (PR) and Punta Chacaya (PC) within 10-50 m water-depth gradient. PR sediments were organic matter rich (21.1% of TOM at 50 m) and overlaid with low-oxygen waters (<0.06 ml O2/L bottom layer) compared with PC. In general, HMs like Al, Ni, Cd, As and Pb tended to increase in concentration with depth in PR, while the opposite pattern was observed in PC. In addition, PR presented a higher number of unique families (72) compared to PC (35). Among the top ten microbial families, Desulfobulbaceae (4.6% vs. 3.2%), Flavobacteriaceae (2.8% vs. 2.3%) and Anaerolineaceae (3.3% vs. 2.3%) dominated in PR, meanwhile Actinomarinales_Unclassified (8.1% vs. 4.2%) and Sandaracinaceae (4.4% vs. 2.0%) were more abundant in PC. Multivariate analyses confirmed that water depth-related variation was a good proxy for oxygen conditions and metal concentrations, explaining the structure of benthic microbial assemblages. Cd, Ni, As and Pb showed uniformly positive associations with communities that represented the keystone taxa in the co-occurrence network, including Anaerolineaceae, Thiotrichaceae, Desulfobulbaceae, Desulfarculaceae and Bacteroidales_unclassified communities. Collectively, these findings provide new insights for establishing the ecological interconnections of benthic microorganisms in response to metal contamination in a coastal upwelling environment.

Greenhouse gases and biogeochemical diel fluctuations in a high-altitude wetland.

The landscapes of high-altitude wetland ecosystems are characterized by different kinds of aquatic sites, including ponds holding conspicuous microbial life. Here, we examined a representative pond of the wetland landscape for dynamics of greenhouse gases, and their association with other relevant biogeochemical conditions including diel shifts of microbial communities' structure and activity over two consecutive days. Satellite image analysis indicates that the area of ponds cover 238 of 381.3 Ha (i.e., 62.4%), representing a significant landscape in this wetland. Solar radiation, wind velocity and temperature varied daily and between the days sampled, influencing the biogeochemical dynamics in the pond, shifting the pond reservoir of inorganic versus dissolved organic nitrogen/phosphorus bioavailability, between day 1 and day 2. Day 2 was characterized by high dissolved organic nitrogen/phosphorus and N2O accumulation. CH4 presented a positive excess showing maxima at hours of high radiation during both days. The microbial community in the sediment was diverse and enriched in keystone active groups potentially related with GHG recycling including bacteria and archaea, such as Cyanobacteria, Verrucomicrobia, Rhodobacterales and Nanoarchaeaota (Woesearchaeia). Archaea account for the microbial community composition changes between both days and for the secondary productivity in the water measured during day 2. The results indicate that an intense recycling of organic matter occurs in the pond systems and that the activity of the microbial community is correlated with the availability of nutrients. Together, the above results indicate a net sink of CO2 and N2O, which has also been reported for other natural and artificial ponds. Overall, our two-day fluctuation study in a representative pond of a high-altitude wetland aquatic landscape indicates the need to explore in more detail the short-term besides the long-term biogeochemical variability in arid ecosystems of the Andes plateau, where wetlands are hotspots of life currently under high anthropogenic pressure.

Endangered Salares: micro-disasters in Northern Chile.

This article emerges from a transdisciplinary collaboration between a micro-biologist and an anthropologist deeply concerned with the protection of endangered salares (saltpans) in northern Chile. Our aim is to establish the concept of "micro-disaster" as a tool for examining how extractivism is disrupting salares and their "deep-time" microbial ecologies. These ecologies are key for understanding early events on Earth, as their evolution enabled the oxygenation of the planet 2.5 billion years ago and caused the biodiversity explosion. By considering how being human involves being microorganismal - and how human time is entangled with microorganismic time -, this article connects neoliberal extractivist history with geo-biological evolutionary history. "Micro-disasters" therefore affect us deeply as complex humans, and oblige us to develop further a planet-centered mode of collaborating, thinking, feeling, and acting. In the context of this special issue on extinction, we insist that concerns over extinction must be considered in continuity with deep-time ecologies. We propose to rethink humans as an "environmentally complex we" simultaneously entangled with historical experiential time and microbial "deep-time."

Este artigo surge de uma colaboração transdisciplinar entre uma microbióloga e um antropólogo profundamente preocupados com a proteção de salares (salinas) em perigo no norte do Chile. Nosso objetivo é estabelecer o conceito de "microdesastre" como uma ferramenta para examinar como o extrativismo está perturbando os salares e suas ecologias microbianas de 'tempo-profundo'. Essas ecologias são fundamentais para compreender os primeiros eventos na Terra, pois sua evolução permitiu a oxigenação do planeta há 2,5 bilhões de anos e causou a explosão da biodiversidade. Ao considerar como ser humano envolve ser microorganísmico ­ e como o tempo humano está enredado com o tempo microorganísmico, este artigo conecta a história extrativista neoliberal com a história evolutiva geo-biológica. Os "microdesastres," portanto, nos afetam profundamente como humanos complexos, e nos obrigam a desenvolver ainda mais um modo de colaboração, pensamento, sentimento e ação centrado no planeta. No contexto desta edição especial sobre a extinção, insistimos que as preocupações com a extinção devem ser consideradas em continuidade com as ecologias do tempo profundo. Propomos repensar o ser humano como um "nós ambientalmente complexo" simultaneamente emaranhados com o tempo histórico experiencial e o "tempo profundo" microbiano.

Este artículo es fruto de la colaboración transdisciplinaria entre una microbióloga y un antropólogo fuertemente preocupados por la protección de salares del norte de Chile que actualmente corren peligro de extinción. Nuestro objetivo es proponer el concepto de "micro-desastre" como herramienta que examina los modos en que el extractivismo está alterando a estos salares y a sus ecologías microbianas de tiempo-profundo. Estas ecologías son clave para entender eventos tempranos en la Tierra, en tanto la evolución de ellas hizo posible la oxigenación del planeta hace 2500 millones de años, causando así la explosión de la biodiversidad. Considerando como el ser humano implica un ser microorganísmico ­ y como el tiempo humano está enredado con un tiempo micro-organísmico ­ este artículo conecta la historia extractivista neoliberal chilena con la historia de la evolución geo-biológica. Por lo tanto, los "micro-desastres" nos afectan fuertemente como humanos complejos, y nos obligan a desarrollar, una y otra vez, un modo de colaborar, pensar, sentir y actuar fuertemente centrado en el planeta. En el contexto de este número especial focalizado en extinción, insistimos en la necesidad de considerar los problemas puestos por la posibilidad de extinción en continuidad con ecologías de tiempo-profundo. Proponemos repensarnos como humanos como un "nosotros ambientalmente complejo," simultáneamente enredado en el tiempo histórico experiencial y el tiempo microbiano profundo.

Connectivity of bacterial assemblages along the Loa River in the Atacama Desert, Chile.

The Loa River is the only perennial artery that crosses the Atacama Desert in northern Chile. It plays an important role in the ecological and economic development of the most water-stressed region, revealing the impact of the mining industry, which exacerbate regional water shortages for many organisms and ecological processes. Despite this, the river system has remained understudied. To our knowledge, this study provides the first effort to attempt to compare the microbial communities at spatial scale along the Loa River, as well as investigate the physicochemical factors that could modulate this important biological component that still remains largely unexplored. The analysis of the spatial bacterial distribution and their interconnections in the water column and sediment samples from eight sites located in three sections along the river catchment (upper, middle and lower) was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. Among a total of 543 ASVs identified at the family level, over 40.5% were cosmopolitan in the river and distributed within a preference pattern by the sediment substrate with 162 unique ASVs, while only 87 were specific to the column water. Bacterial diversity gradually decreased from the headwaters, where the upper section had the largest number of unique families. Distinct groupings of bacterial communities often associated with anthropogenic disturbance, including Burkholderiaceae and Flavobacteriaceae families were predominant in the less-impacted upstream section. Members of the Arcobacteraceae and Marinomonadaceae were prominent in the agriculturally and mining-impacted middle sector while Rhodobacteraceae and Coxiellaceae were most abundant families in downstream sites. Such shifts in the community structure were also related to the influence of salinity, chlorophyll, dissolved oxygen and redox potential. Network analyses corroborated the strong connectivity and modular structure of bacterial communities across this desert river, shedding light on taxonomic relatedness of co-occurring species and highlighting the need for planning the integral conservation of this basin.

Determinants of Copper Resistance in Acidithiobacillus Ferrivorans ACH Isolated from the Chilean Altiplano.

The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0-800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs.

Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile.

Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.