Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems

Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon and nutrient cycling. To date, however, a comparative analysis of their taxonomic and functional diversity that compares the major ecosystems on Earth (soil, freshwater and marine systems) is missing. Here, we present a comparison of protist diversity based on standardized high throughput 18S rRNA gene sequencing of soil, freshwater and marine environmental DNA. Soil and freshwater protist communities were more similar to each other than to marine protist communities, with virtually no overlap of Operational Taxonomic Units (OTUs) between terrestrial and marine habitats. Soil protists showed higher γ diversity than aquatic samples. Differences in taxonomic composition of the communities led to changes in a functional diversity among ecosystems, as expressed in relative abundance of consumers, phototrophs and parasites. Phototrophs (eukaryotic algae) dominated freshwater systems (49% of the sequences) and consumers soil and marine ecosystems (59% and 48%, respectively). The individual functional groups were composed of ecosystem- specific taxonomic groups. Parasites were equally common in all ecosystems, yet, terrestrial systems hosted more OTUs assigned to parasites of macro-organisms while aquatic systems contained mostly microbial parasitoids. Together, we show biogeographic patterns of protist diversity across major ecosystems on Earth, preparing the way for more focused studies that will help understanding the multiple roles of protists in the biosphere.

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands

Bacteria play critical roles in peatland ecosystems. However, very little is known of how habitat heterogeneity affects the structure of the bacterial communities in these ecosystems. Here, we used amplicon sequencing of the 16S rRNA and nifH genes to investigate phylogenetic diversity and bacterial community composition in three different sub-Antarctic peat bog aquatic habitats: Sphagnum magellanicum interstitial water, and water from vegetated and non-vegetated pools. Total and putative nitrogen-fixing bacterial communities from Sphagnum interstitial water differed significantly from vegetated and non-vegetated pool communities (which were colonized by the same bacterial populations), probably as a result of differences in water chemistry and biotic interactions. Total bacterial communities from pools contained typically aquatic taxa, and were more dissimilar in composition and less species rich than those from Sphagnum interstitial waters (which were enriched in taxa typically from soils), probably reflecting the reduced connectivity between the former habitats. These results show that bacterial communities in peatland water habitats are highly diverse and structured by multiple concurrent factors.

Perils of life on the edge: Climatic threats to global diversity patterns of wetland macroinvertebrates

Climate change is rapidly driving global biodiversity declines. How wetland macroinvertebrate assemblages are responding is unclear, a concern given their vital function in these ecosystems. Using a data set from 769 minimally impacted depressional wetlands across the globe (467 temporary and 302 permanent), we evaluated how temperature and precipitation (average, range, variability) affects the richness and beta diversity of 144 macroinvertebrate families. To test the effects of climatic predictors on macroinvertebrate diversity, we fitted generalized additive mixed-effects models (GAMM) for family richness and generalized dissimilarity models (GDMs) for total beta diversity. We found non-linear relationships between family richness, beta diversity, and climate. Maximum temperature was the main climatic driver of wetland macroinvertebrate richness and beta diversity, but precipitation seasonality was also important. Assemblage responses to climatic variables also depended on wetland water permanency. Permanent wetlands from warmer regions had higher family richness than temporary wetlands. Interestingly, wetlands in cooler and dry-warm regions had the lowest taxonomic richness, but both kinds of wetlands supported unique assemblages. Our study suggests that climate change will have multiple effects on wetlands and their macroinvertebrate diversity, mostly via increases in maximum temperature, but also through changes in patterns of precipitation. The most vulnerable wetlands to climate change are likely those located in warm-dry regions, where entire macroinvertebrate assemblages would be extirpated. Montane and high-latitude wetlands (i.e., cooler regions) are also vulnerable to climate change, but we do not expect entire extirpations at the family level.

Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland

Bacterioplankton communities inhabiting peatlands have the potential to influence local ecosystem functions. However, most microbial ecology research in such wetlands has been done in ecosystems (mostly peat soils) of the Northern Hemisphere, and very little is known of the factors that drive bacterial community assembly in other regions of the world. In this study, we used high-throughput sequencing to analyse the structure of the bacterial communities in five pools located in a sub-Antarctic peat bog (Tierra del Fuego, Argentina), and tested for relationships between bacterial communities and environmental conditions. Bacterioplankton communities in peat bog pools were diverse and dominated by members of the Proteobacteria, Actinobacteria, Bacteroidetes and Verrucomicrobia. Community structure was largely explained by differences in hydrological connectivity, pH and nutrient status (ombrotrophic versus minerotrophic pools). Bacterioplankton communities in ombrotrophic pools showed phylogenetic clustering, suggesting a dominant role of deterministic processes in shaping these assemblages. These correlations between habitat characteristics and bacterial diversity patterns provide new insights into the factors regulating microbial populations in peatland ecosystems.

Microdiverse bacterial clades prevail across Antarctic wetlands

Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.

A reassessment of testate amoebae diversity in Tierra del Fuego peatlands: Implications for large scale inferences

Testate amoebae are a diverse group of shelled protists frequently used as model organisms in microbial biogeography. Relatively few species have been reported for the Southern Hemisphere, however, it remains unclear whether this lower diversity is real or an artifact of under-sampling or misidentifications, which would reduce their potential to address macroecological questions. We evaluated testate amoebae diversity from the full range of habitats occurring within two Tierra del Fuego peatlands and compared it with the reported diversity for the area and from the Northern Hemisphere peatlands. We recorded 87 species, of which 69 are new for the region and 45 of them probably new to science and likely to have restricted geographical distributions. Combined with previous studies, the total diversity of testate amoebae only from Tierra del Fuego peatlands now reaches 119, as compared with 183 reported from all Northern Hemisphere peatlands. Our results demonstrate that the number of Gondwanian and Neotropical endemic testate amoeba may be substantially higher than currently known. Previous reports of Holarctic taxa in Tierra del Fuego may result from forcing the identification of morphotypes to the descriptions in the most common literature (force-fitting) South American species into species common in literature from other regions.

The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution

As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%–97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco‐evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.

Hydrology-driven seasonal changes in the phytoplankton of a subtropical river (Riacho Formosa, Argentina)

The Riacho Formosa is one of many autochtonous watercourses running along the subtropical region of the Wet Chaco Plains and draining into Paraguay River. Their typical hydrological cycle is characterized by a late winter low phase and a high phase throughout the warm season. As part of a baseline characterization, the composition and structure of the phytoplankton were studied in relation to river depth, water temperature, pH, conductivity and transparency through 4 seasonal samplings between June 2015 and March 2016. A rich phytoplankton community (338 taxa) was revealed in this study. A few species of Cryptophyceae and Euglenophyceae dominated the community, especially during low waters. A cluster analysis showed that community compositions were more dissimilar over time than along the watercourse, and were spatially more homogeneous during high waters. A canonical correspondence analysis showed that environmental features significantly explained 42.6% of the total variance of species data (p= 0.004). We conclude that phytoplankton responds to hydrological changes through a high species turnover, with dominance peaks of euryhaline, shadow adapted and organic matter exploiting taxa during low waters.