Planktonic microbial communities from microbialite-bearing lakes sampled along a salinity-alkalinity gradient.

Continental freshwater systems are particularly vulnerable to environmental variation. Climate change-induced desertification and the anthropogenic exploitation of hydric resources result in the progressive evaporation and salinization of inland water bodies in many areas of the globe. However, how this process impacts microbial communities and their activities in biogeochemical cycles is poorly known. Here, we take a space-for-time substitution approach and characterize the prokaryotic and eukaryotic microbial communities of two planktonic cell-size fractions (0.2-5 µm and 5-30 µm) from lakes of diverse trophic levels sampled along a salinity-alkalinity gradient located in the Trans-Mexican Volcanic Belt (TMVB). We applied a 16S/18S rRNA gene metabarcoding strategy to determine the microbial community composition of 54 samples from 12 different lakes, from the low-salinity lake Zirahuén to the hypersaline residual ponds of Rincón de Parangueo. Except for systems at both extremes of the salinity gradient, most lakes along the evaporation trend bear actively forming microbialites, which harbor microbial communities clearly distinct from those of plankton. Several lakes were sampled in winter and late spring and the crater lakes Alchichica and Atexcac were sampled across the water column. Physicochemical parameters related to salinity-alkalinity were the most influential drivers of microbial community structure whereas trophic status, depth, or season were less important. Our results suggest that climate change and anthropogenic-induced hydric deficit could significantly affect microbial communities, potentially altering ecosystem functioning.

Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient.

Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.

Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake.

Identifying which abiotic and biotic factors determine microbial community assembly is crucial to understand ecological processes and predict how communities will respond to environmental change. While global surveys aim at addressing this question in the world's oceans, equivalent studies in large freshwater systems are virtually lacking. Being the oldest, deepest and most voluminous freshwater lake on Earth, Lake Baikal offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Here, we characterized the structure of planktonic microbial eukaryotic communities (0.2-30 µm cell size) along a North-South latitudinal gradient (~600 km) from samples collected in coastal and pelagic waters and from surface to the deepest zones (5-1400 m) using an 18S rRNA gene metabarcoding approach. Our results show complex and diverse protist communities dominated by alveolates (ciliates and dinoflagellates), ochrophytes and holomycotan lineages, with cryptophytes, haptophytes, katablepharids and telonemids in moderate abundance and many low-frequency lineages, including several typical marine members, such as diplonemids, syndinians and radiolarians. Depth had a strong significant effect on protist community stratification. By contrast, the effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic communities were significantly more interconnected than communities from the dark water column and suggest specific biotic interactions between autotrophic, heterotrophic and parasitic lineages that influence protist community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, our comprehensive protist survey constitutes a useful reference to monitor ongoing community shifts.

Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns.

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond.

Modern phototrophic microbial mats are complex communities often used as analogs of major Precambrian ecosystems. Characterizing biotic, notably metabolic, interactions among different microbial mat members is essential to gain insights into the ecology and biogeochemistry of these systems. We applied 16S/18S rRNA metabarcoding approaches to characterize the structure of archaea, bacteria and protist communities from microbial mats collected along strong physicochemical (oxygen, salinity, temperature, depth) gradients in a shallow pond at the salar de Llamara (Chile). All mats were highly diverse, including members of virtually all known high-rank eukaryotic and prokaryotic taxa but also many novel lineages. Bacterial candidate divisions accounted for almost 50% of sequences in deeper mats, while Archaea represented up to 40% of sequences in some mat layers. Molecular phylogenetic analyses revealed six novel deeply divergent archaeal groups, along abundant and diverse Pacearchaeota and Woesearchaeota. Multivariate statistical analyses showed that local environmental conditions strongly influenced community composition. Co-occurrence network structure was markedly different between surface mats located in the oxygenated zone and mats located in transition and anoxic water layers. We identified potential biotic interactions between various high- and low-rank taxa. Notably, a strong positive correlation was observed between Lokiarchaeota and the poorly known candidate bacterial division TA06.

Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient.

Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.

Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems.

Although inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well known. Some molecular surveys of lakes exist, but little information is available from smaller, shallower and often ephemeral freshwater systems, despite their global distribution and ecological importance. We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 µm size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France. Our study revealed a wide diversity of small protists, with 812 stringently defined operational taxonomic units (OTUs) belonging to the recognized eukaryotic supergroups (SAR--Stramenopiles, Alveolata, Rhizaria--Archaeplastida, Excavata, Amoebozoa, Opisthokonta) and to groups of unresolved phylogenetic position (Cryptophyta, Haptophyta, Centrohelida, Katablepharida, Telonemida, Apusozoa). Some OTUs represented deep-branching lineages (Cryptomycota, Aphelida, Colpodellida, Tremulida, clade-10 Cercozoa, HAP-1 Haptophyta). We identified several lineages previously thought to be marine including, in addition to MAST-2 and MAST-12, already detected in freshwater, MAST-3 and possibly MAST-6. Protist community structures were different in the five ecosystems. These differences did not correlate with geographical distances, but seemed to be influenced by environmental parameters.

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.

Rapid formation of mature microbialites in Lake Alchichica, Mexico.

Microbialites are emblematic sedimentary rocks formed by phylogenetically and metabolically complex microbial communities thriving under specific physicochemical conditions. Most microbialites are photosynthesis-based ecosystems frequently formed by carbonates, thereby capturing inorganic carbon in the form of both, organic matter and mineral precipitates. However, little is known about the amount of sequestered carbon and the kinetics of the process, that is, microbialite growth rate. To assess microbialite growth rate and the influence of substrates on carbonate formation in Alchichica, an alkaline crater lake harbouring well-developed carbonate microbialites, we incubated in situ sterilized Nylon mesh, hydromagnesite and aragonite crystals, and bleached-coral aragonite for 2 years. We observed the rapid formation of nascent hydromagnesite and aragonite-containing microbialites on Nylon mesh, with an average growth rate of ~0.6 (and up to 1) mm year-1 . By contrast, only thin (< 0.2 mm) biofilms developed on exposed hydromagnesite and aragonite crystals and bleached-coral aragonite, suggesting decoupled microbial colonization and biomineralization and/or potential interference of those mineral surfaces with new carbonate nucleation. Microbial communities associated with 2-year-old microbialites and biofilms were fully comparable to mature communities populating Lake Alchichica indigenous microbialites.

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake.

Lake Baikal is the deepest (~1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a ~600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.

Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania.

Movile Cave is a small system of partially inundated galleries in limestone settings close to the Black Sea in Southeast Romania. Isolated from the surface for 6 million years, its sulfidic, methane and ammonia-rich waters harbour unique chemosynthetic prokaryotic communities that include sulphur and ammonium-metabolizing chemolithotrophs, methanogens, methanotrophs and methylotrophs. The cave also harbours cave-dwelling invertebrates and fungi, but the diversity of other microbial eukaryotes remained completely unknown. Here, we apply an 18S rRNA gene-based metabarcoding approach to study the composition of protist communities in floating microbial mats and plankton from a well-preserved oxygen-depleted cave chamber. Our results reveal a wide protist diversity with, as dominant groups, ciliates (Alveolata), Stramenopiles, especially bicosoecids, and jakobids (Excavata). Ciliate sequences dominated both, microbial mats and plankton, followed by either Stramenopiles or excavates. Stramenopiles were more prominent in microbial mats, whereas jakobids dominated the plankton fraction of the oxygen-depleted water column. Mats cultured in the laboratory were enriched in Cercozoa. Consistent with local low oxygen levels, Movile Cave protists are most likely anaerobic or microaerophilic. Several newly detected OTU clades were very divergent from cultured species or environmental sequences in databases and represent phylogenetic novelty, notably within jakobids. Movile Cave protists likely cover a variety of ecological roles in this ecosystem including predation, parasitism, saprotrophy and possibly diverse prokaryote-protist syntrophies.

Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area.

Microbial life has adapted to various individual extreme conditions; yet, organisms simultaneously adapted to very low pH, high salt and high temperature are unknown. We combined environmental 16S/18S ribosomal RNA gene metabarcoding, cultural approaches, fluorescence-activated cell sorting, scanning electron microscopy and chemical analyses to study samples along such unique polyextreme gradients in the Dallol-Danakil area in Ethiopia. We identified two physicochemical barriers to life in the presence of surface liquid water defined by (1) high chaotropicity-low water activity in Mg2+/Ca2+-dominated brines and (2) hyperacidity-salt combinations (pH ~0/NaCl-dominated salt saturation). When detected, life was dominated by highly diverse ultrasmall archaea that were widely distributed across phyla with and without previously known halophilic members. We hypothesize that a high cytoplasmic K+-level was an original archaeal adaptation to hyperthermophily, subsequently exapted during several transitions to extreme halophily. We detect active silica encrustment/fossilization of cells but also abiotic biomorphs of varied chemistry. Our work helps circumscribing habitability and calls for cautionary interpretations of morphological biosignatures on Earth and beyond.

Resilience of Freshwater Communities of Small Microbial Eukaryotes Undergoing Severe Drought Events.

Small and shallow aquatic ecosystems such as ponds and streams constitute a significant proportion of continental surface waters, especially in temperate zones. In comparison with bigger lakes and rivers, they harbor higher biodiversity but they also exhibit reduced buffering capacity face to environmental shifts, such that climate global change can affect them in a more drastic way. For instance, many temperate areas are predicted to undergo droughts with increasing frequency in the near future, which may lead to the temporal desiccation of streams and ponds. In this work, we monitored temporal dynamics of planktonic communities of microbial eukaryotes (cell size range: 0.2-5 µm) in one brook and one pond that experienced recurrent droughts from 1 to 5 consecutive months during a temporal survey carried out monthly for 2 years based on high-throughput 18S rDNA metabarcoding. During drought-induced desiccation events, protist communities present in the remaining dry sediment, though highly diverse, differed radically from their planktonic counterparts. However, after water refill, the aquatic protist assemblages recovered their original structure within a month. This rapid recovery indicates that these eukaryotic communities are resilient to droughts, most likely via the entrance in dormancy. This property is essential for the long-term survival and functional stability of small freshwater ecosystems.

Marked seasonality and high spatial variability of protist communities in shallow freshwater systems.

Small eukaryotes have key roles in aquatic ecosystems, influencing their local environment, global biogeochemical cycles and climate. Their impact depends on community structure, which varies along time. However, very few studies take into account temporal variation. This is especially true for small, shallow freshwater systems, which remain largely understudied despite their wide variety, global surface and intense microbial activity. We have monthly followed changes in the community structure of small microbial eukaryotes (0.2-5 µm cell diameter) for 2 years in four ponds and one brook located in North-Western France based on massive 18S rDNA amplicon 454 pyrosequencing. We detected a total of 3742 stringently defined operational taxonomic units (OTUs) encompassing all recognized eukaryotic supergroups and lineages of uncertain affiliation. Although geographically close, protist communities in the five ecosystems were contrasting, with very few shared OTUs, suggesting that environmental selection mainly drives community structure. The temporal dynamics of different high-rank taxa appeared complex and rapid at monthly scales. Despite this, a clear and reproducible seasonality was observed. As expected, low-abundance OTUs dominated the community. Although some of them appeared sporadically or remained at low frequencies during the survey, others occasionally reached relatively high abundances, sometimes recurrently. This shows that at least a fraction of low-abundance eukaryotes constitutes a seed bank. The annual proportion of primary producers, free-living heterotrophs and parasites appeared remarkably constant among the different ecosystems, suggesting underlying trends of ecosystem carrying capacity for these functional groups.

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites.

Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

The phylogeny and biogeographic history of ashes (fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees.

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.