Increasing diversity and biotic homogenization of lake plankton during recovery from acidification

Determining biodiversity responses to environmental change, such as acidification, is critical for ecosystem projections under future global change scenarios. Here, we analyzed three plankton communities of phytoplankton, crustaceans and rotifers in 28 lakes in the Adirondack Park, USA, during 1994-2012, and examined the spatiotemporal trends in their alpha and beta diversity during recovery from acidification. For all plankton assemblages, Shannon diversity increased towards recent years and high lake pH, and there was an increasing community dissimilarity with pH changes. The spatial mean Bray-Curtis dissimilarities across all lakes decreased over time for phytoplankton and rotifers leading to an increase in spatial homogenization. Such a homogenization cooccurred however with the overall increasing diversity in this region, which contrasts with the previous classic view that homogenization is mainly driven by loss of species and results in biodiversity loss. We further observed lower temporal mean beta diversity in low-pH lakes for crustaceans and rotifers, but not for phytoplankton. Generally, spatial and temporal mean beta diversity of the three taxonomic groups were primarily driven by lake-water ion variables, and rotifers were also constrained by nutrients and climate. Collectively, our results show how and why plankton community compositions vary over space along with acidification recovery, and further highlight the importance of spatiotemporal studies combined with long-term monitoring programs in assessing biodiversity change during the recovery of disturbed ecosystems.

Planktonic ciliate community driven by environmental variables and cyanobacterial blooms: A 9-year study in two subtropical reservoirs

It is well-established that environmental variability and cyanobacterial blooms have major effects on the assembly and functioning of bacterial communities in both marine and freshwater habitats. It remains unclear, however, how the ciliate community responds to such changes over the long-term, particularly in subtropical lake and reservoir ecosystems. We analysed 9-year planktonic ciliate data series from the surface water of two subtropical reservoirs to elucidate the role of cyanobacterial bloom and environmental variabilities on the ciliate temporal dynamics. We identified five distinct periods of cyanobacterial succession in both reservoirs. Using multiple time-scale analyses, we found that the interannual variability of ciliate communities was more strongly related to cyanobacterial blooms than to other environmental variables or to seasonality. Moreover, the percentage of species turnover across cyanobacterial bloom and non-bloom periods increased significantly with time over the 9-year period. Phylogenetic analyses further indicated that 84 %-86 % of ciliate community turnover was governed by stochastic dispersal limitation or undominated processes, suggesting that the ciliate communities in subtropical reservoirs were mainly controlled by neutral processes. However, short-term blooms increased the selection pressure and drove 30 %-53 % of the ciliate community turnover. We found that the ciliate community composition was influenced by environmental conditions with nutrients, cyanobacterial biomass and microzooplankton having direct and/or indirect significant effects on the ciliate taxonomic or functional community dynamics. Our results provide new insights into the long-term temporal dynamics of planktonic ciliate communities under cyanobacterial bloom disturbance.

Decoupling of respiration rates and abundance in marine prokaryoplankton

The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.

Plankton diversity in Anthropocene: Shipping vs. aquaculture along the eastern Adriatic coast assessed through DNA metabarcoding

Coastal ecosystems globally are exposed to the most pervasive anthropogenic activities, caused by a suite of human infrastructure and enterprises such as shipping ports, aquaculture facilities, fishing, and tourism. These anthropogenic activities may lead to changes in ecosystem biodiversity, followed by loss of ecosystem functioning and services. Shipping industry and aquaculture have also been recognized as the main vectors for introduction of marine non-indigenous species (NIS) worldwide. In this study, we used DNA metabarcoding-based methods to investigate plankton biodiversity under varying anthropogenic pressures (shipping and bivalve aquaculture) along the eastern Adriatic coast (the northernmost part of the Mediterranean Sea). Our comparative assessment revealed similar community structures among investigated coastal locations (Northern, Central and Southern Adriatic). When the whole plankton communities were considered, they did not differ significantly between port and aquaculture sites. However, the proportion of the unique zOTUs in the port samples was remarkably higher than that in aquaculture sites (40.5% vs 8.2%), indicating that port areas may receive higher abundance and species richness of NIS than aquaculture sites. Further important difference between the two types of anthropogenically impacted habitats was a high abundance of three notorious invaders - M. leidyi, M. gigas, and H. elegans in late summer at the aquaculture site in Northern Adriatic. Therefore, the plankton community of the area is under pressure not only from aquaculture activities, but also establishment of NIS. Port areas are probably under greater introduction pressure from NIS, but aquaculture sites may experience greater community changes due to their establishment.

Triton, a new species-level database of Cenozoic planktonic foraminiferal occurrences

Planktonic foraminifera are a major constituent of ocean floor sediments, and thus have one of the most complete fossil records of any organism. Expeditions to sample these sediments have produced large amounts of spatiotemporal occurrence records throughout the Cenozoic, but no single source exists to house these data. We have therefore created a comprehensive dataset that integrates numerous sources for spatiotemporal records of planktonic foraminifera. This new dataset, Triton, contains >500,000 records and is four times larger than the previous largest database, Neptune. To ensure comparability among data sources, we have cleaned all records using a unified set of taxonomic concepts and have converted age data to the GTS 2020 timescale. Where ages were not absolute (e.g. based on biostratigraphic or magnetostratigraphic zones), we have used generalised additive models to produce continuous estimates. This dataset is an excellent resource for macroecological and macroevolutionary studies, particularly for investigating how species responded to past climatic changes.

A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin

Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.

Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands

Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

BACKGROUND

Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe.

RESULTS

Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion.

CONCLUSIONS

Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.

Ecological status of a freshwater tectonic lake of the indo-burmese province: Implications for livelihood development

Tectonic lakes are among the most geologically fascinating and environmentally versatile hydrobiological systems found on the earth's surface. We conducted a study on the limnology of Tasek Lake, a tectonic lake located in the Indo-Burma Province of the South Asian region. Physico-chemical parameters of the lake's water along with its plankton were considered for the study. Their relationship was analysed by understanding their seasonal variations and through linear regression models. The water quality index (WQI), plankton diversity indices and canonical correspondence analysis (CCA) were computed. The ichthyofaunal diversity was also studied to get an insight into the lake's fishery potential. A preliminary assessment on the economic feasibility of converting Tasek Lake into a fishery was also completed. Results indicate moderate eutrophication in the lake and the plankton population is observed to be rich and abundant. The WQI value confirms the water to be of "very poor" quality. The CCA was done to analyze the relationships of physico-chemical parameters with months and seasons, and the relation between seasons and plankton assemblages. Results corroborate the results of WQI. Identified fish population suggest ample fishery potential of the lake. The economic assessment reveals that in order to maintain the ecological sustainability of the lake, it should be transformed into a recreational fishery, following a catch-and-release model. The study calls for urgent restoration of the lake so that not only its pristine ecology is survived but also its fishery potential is sustainably harnessed and local livelihood is improved.

The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle

Pteropods are a group of planktonic gastropods that are widely regarded as biological indicators for assessing the impacts of ocean acidification. Their aragonitic shells are highly sensitive to acute changes in ocean chemistry. However, to gain insight into their potential to adapt to current climate change, we need to accurately reconstruct their evolutionary history and assess their responses to past changes in the Earth's carbon cycle. Here, we resolve the phylogeny and timing of pteropod evolution with a phylogenomic dataset (2,654 genes) incorporating new data for 21 pteropod species and revised fossil evidence. In agreement with traditional taxonomy, we recovered molecular support for a division between "sea butterflies" (Thecosomata; mucus-web feeders) and "sea angels" (Gymnosomata; active predators). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled, and unshelled groups, diverged in the mid- to late Cretaceous. Hence, these clades originated prior to and subsequently survived major global change events, including the Paleocene-Eocene Thermal Maximum (PETM), the closest analog to modern-day ocean acidification and warming. Our findings indicate that planktonic aragonitic calcifiers have shown resilience to perturbations in the Earth's carbon cycle over evolutionary timescales.

Periodic density as an endpoint of customized plankton community responses to petroleum hydrocarbons: A level of toxic effect should be matched with a suitable time scale

As an endpoint of community response to contaminants, average periodic density of populations (APDP) has been introduced to model species interactions in a community with 4 planktonic species. An ecological model for the community was developed by means of interspecific relationship including competition and predation to calculate the APDP. As a case study, we reported here the ecotoxicological effects of petroleum hydrocarbons (PHC) collected from Bohai oil field on densities of two algae, Platymonas subcordiformis and Isochrysis galbana, a rotifer, Brachionus plicatilis, and of a cladocera, Penilia avirostris, in single species and a microcosm experiment. Time scales expressing toxic effect increased with increasing levels of toxic effect from molecule to community. Remarkable periodic changes in densities were found during the tests in microcosm experiment, revealing a strong species reaction. The minimum time scale characterizing toxic effect at a community level should be the common cycle of population densities of the microcosm. In addition, the cycles of plankton densities shortened in general with increasing PHC, showing an evident toxic effect on the microcosm. Using APDP as the endpoint, a threshold concentration for the modeled microcosm was calculated to be 0.404 mg-PHC L^-1. The APDP was found to be more sensitive and reliable than the standing crops of populations as the endpoint. This indicated that the APDP, an endpoint at the community level, could be quantitatively related to the endpoints at the population level, and led to the quantitative concentration-toxic effect relationship at the community level.

Femtoplankton: What's New?

Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010-2020) of high abundances of biomimetic mineral-organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.

Subtle bacterioplankton community responses to elevated CO2 and warming in the oligotrophic South Pacific gyre

Bacterioplankton play a critical role in primary production, carbon cycling, and nutrient cycling in the oligotrophic ocean. To investigate the effect of elevated CO₂ and warming on the composition and function of bacterioplankton communities in oligotrophic waters, we performed two trace-metal clean deck board incubation experiments during the New Zealand GEOTRACES transect of the South Pacific gyre (SPG). High-throughput amplicon sequencing of the 16S rRNA gene revealed that bacterioplankton community composition was distinct between the fringe and ultra-oligotrophic centre of the SPG and changed consistently in response to elevated CO₂ at the ultra-oligotrophic centre but not at the mesotrophic fringe of the SPG. The combined effects of elevated CO₂ and warming resulted in a high degree of heterogeneity between replicate communities. Community-level protein synthesis rates (³ H-Leucine incorporation) and bacterioplankton abundance were not affected by elevated CO₂ alone or in combination with warming at the fringe or ultra-oligotrophic centre of the SPG. These data suggest bacterioplankton community responses to elevated CO₂ may be modulated by nutrient regimes in open ocean ecosystems and highlight the need for further investigation in expanding oligotrophic subtropical gyres.

Subtropical to temperate late Neogene to Quaternary planktic foraminiferal biostratigraphy across the Kuroshio Current Extension, Shatsky Rise, northwest Pacific Ocean

Planktic foraminiferal biostratigraphic zonation schemes are critical for providing first-order relative age control in deep-sea sediments and provide the basis on which to interpret evolutionary dynamics through time. Over the previous decades, the majority of published biostratigraphic zonation schemes focused on the tropical regions of the world. The mid-latitude or temperate regions, especially of the northwest Pacific, have been understudied in terms of recording plankton occurrences. Lack of detailed biostratigraphic studies have largely left out this region from plankton evolutionary analyses, thus how this part of the world ocean, which is characterized by the Kuroshio Current Extension (KCE), may contribute to global plankton biodiversity is unknown. In this study, we present the first magnetostratigraphically-calibrated late Neogene to Quaternary (15.12-0 Ma) planktic foraminiferal zonation schemes from the northwest Pacific for three Ocean Drilling Program Leg 198 holes (1207A, 1208A, and 1209A) that span the KCE. We utilize previously published warm subtropical, cool subtropical, and temperate zonation schemes from the southwest Pacific, with modifications. We find examples of significant diachroneity among primary marker taxa used to construct biozones at the three northwest Pacific sites, which ranges from 0.075 to 2.29 million years. Comparison of our primary datum markers with those of the tropical planktic foraminiferal zonation scheme also reveal diachroneity on the scale of 0.022 to 4.8 million years. We have identified times of intense dissolution in the northwest Pacific, namely in the middle to late Miocene that likely contribute to the observed diachroneity of datums. This study highlights the need for regionally specific mid-latitude biostratigraphic zonation schemes, as diachronous datums and differing assemblages may be hallmarks of oceanic ecotones created by major boundary current systems. These data also provide a framework to characterize local plankton evolutionary dynamics and paleobiogeographic patterns in future studies.

Genetic diversity and connectivity of Flaccisagitta enflata (Chaetognatha: Sagittidae) in the tropical Atlantic ocean (northeastern Brazil)

The phylogeography of the holoplanktonic chaetognath Flaccisagitta enflata was investigated in the Tropical Western Atlantic (TWA). Considering the cosmopolitan range of this species and the fact that its entire life cycle is planktonic, the central hypothesis of this study is that F. enflata exhibits connectivity due to its high dispersal capacity, forming a panmictic population among the study sites. The evaluated areas included neritic (Port of Recife–PR, and Tamandaré - TA) and oceanic (Fernando de Noronha Archipelago—FN, Rocas Atoll—RA, Guará seamount—GS and Saint Peter and Saint Paul’s Archipelago—SPSPA) locations of the Brazilian Blue Amazon. We used COI gene sequences as molecular marker. Partial sequences (425 bp) were obtained for 116 specimens and employed to reconstruct the phylogeny, build an haplotype network, evaluate gene flow through a migration model, and estimate diversity indices, population structuring and demographic history. High levels of haplotype diversity (mean: 0.98) and moderate to high levels of nucleotide diversity (mean: 0.023) were observed. The phylogeny and the haplotype network topologies showed some geographic clustering, indicating local structuring in GS and PR. This finding was supported by the AMOVA high global Φst (0.033, significant) and some pairwise Φst comparisons (7 out of 15 were significantly >0). Significant differences suggested lower levels of connectivity when GS population was compared to those of FN and SPSPA; as well as when TA was compared to FN. These results might be related to particularities of the oceanic dynamics which rules the TWA, sustaining such dissimilarities. Structuring was also observed between PR and all oceanic locations. We hypothesize that the topography of the port inlet, enclosured by a reef barrier, may constrain the water turnover ratio and thus migration rates of F. enflata in the TWA. Accordingly, Migrate-N yielded a four metapopulations model (PR ⇌ TA ⇌ SPSPA+FN ⇌ GS+RA) as the best (highest probability; ~0.90) to represent the structuring of F. enflata in the TWA. Therefore, the null hypothesis of one randomly mating population cannot be accepted. The demographic evaluation demonstrated that the neutral hypothesis of stable populations may not be rejected for most of the locations. This work is the start point to broaden the knowledge on the phylogeography and population genetic structure of a numerically dominant species in the Western Atlantic, with key role in the marine trophic web.

Method for Training Convolutional Neural Networks for In Situ Plankton Image Recognition and Classification Based on the Mechanisms of the Human Eye

In this study, we propose a method for training convolutional neural networks to make them identify and classify images with higher classification accuracy. By combining the Cartesian and polar coordinate systems when describing the images, the method of recognition and classification for plankton images is discussed. The optimized classification and recognition networks are constructed. They are available for in situ plankton images, exploiting the advantages of both coordinate systems in the network training process. Fusing the two types of vectors and using them as the input for conventional machine learning models for classification, support vector machines (SVMs) are selected as the classifiers to combine these two features of vectors, coming from different image coordinate descriptions. The accuracy of the proposed model was markedly higher than those of the initial classical convolutional neural networks when using the in situ plankton image data, with the increases in classification accuracy and recall rate being 5.3% and 5.1% respectively. In addition, the proposed training method can improve the classification performance considerably when used on the public CIFAR-10 dataset.

Disentangling the mechanisms shaping the surface ocean microbiota

BACKGROUND

The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore this, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans.

RESULTS

We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts.

CONCLUSIONS

The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear. Video Abstract.

Norfloxacin pollution alters species composition and stability of plankton communities

Despite recent advances in assessing lethal effects of antibiotics on freshwater organisms, little is known about their potential consequences on community composition and function, which are essential for assessing the ecological risk of these pollutants. Here, we investigated the impact of norfloxacin (NOR) on the short-term (≤ 6 days) dynamics of co-cultured Scenedesmusquadricauda-Chlorella vulgaris and Scenedesmusobliquus-C. vulgaris, and the long-term (≤ 70 days) dynamics of co-cultured S.obliquus-C. vulgaris in experiments with or without grazer Daphnia magna at sublethal antibiotic concentrations (0, 0.5, 2 and 8 mg L^-1). NOR increased the relative abundance of Scenedesmus species in the absence of grazers but exerted opposite effects when Daphnia was present in both short- and long-term experiments due to reduced colony size. Meanwhile, increasing NOR concentrations led to quickly increased total algal density in the initial stage, followed by a sharp decline in the long-term experiment in the absence of grazers; when Daphnia was present, population fluctuations were even larger for both prey and predator species (e.g., grazer extinction at the highest concentration). Thus, NOR affected the outcome of species interactions and decreased temporal stability of plankton ecosystems, suggesting that antibiotics have more extensive impacts than presently recognized.

Oceanic Microplankton Do Not Adhere to the Latitudinal Diversity Gradient

A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged concerning the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. We evaluated microbial planktonic communities along a ~ 15,400-km Pacific Ocean transect with DNA from samples acquired every 2 degrees of latitude within a 3-month period between late August and early November 2003. Next-generation sequencing targeting the Bacteria, Archaea, and Eukarya yielded ~ 10.8 million high-quality sequences. Beta-analysis revealed geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. None of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters, whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on our analyses, environmental factors related to latitude thought to influence various macrofauna may not define microplankton diversity patterns of richness in the global ocean.

Integrated species-phenon trees: visualizing infraspecific diversity within lineages

The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species-phenon tree merges ancestor-descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into "species boxes" and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent-child hierarchy in the integrated tree has been the progressive population of a species-phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others' important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.

Molecular biogeography of planktonic and benthic diatoms in the Yangtze River

BACKGROUND

Diatoms are of great significance to primary productivity in oceans, yet little is known about their biogeographic distribution in oligotrophic rivers.

RESULTS

With the help of metabarcoding analysis of 279 samples from the Yangtze River, we provided the first integral biogeographic pattern of planktonic and benthic diatoms over a 6030 km continuum along the world's third largest river. Our study revealed spatial dissimilarity of diatoms under varying landforms, including plateau, mountain, foothill, basin, foothill-mountain, and plain regions, from the river source to the estuary. Environmental drivers of diatom communities were interpreted in terms of photosynthetically active radiation, temperature, channel slope and nutrients, and human interference. Typical benthic diatoms, such as Pinnularia, Paralia, and Aulacoseira, experienced considerable reduction in relative abundance downstream of the Three Gorges Dam and the Xiluodu Dam, two of the world's largest dams.

CONCLUSIONS

Our study revealed that benthic diatoms are of particular significance in characterizing motile guild in riverine environments, which provides insights into diatom biogeography and biogeochemical cycles in large river ecosystems.

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons

BACKGROUND

The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons.

RESULTS

Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes.

CONCLUSIONS

This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.

Controls on planktonic foraminifera apparent calcification depths for the northern equatorial Indian Ocean

Within the world’s oceans, regionally distinct ecological niches develop due to differences in water temperature, nutrients, food availability, predation and light intensity. This results in differences in the vertical dispersion of planktonic foraminifera on the global scale. Understanding the controls on these modern-day distributions is important when using these organisms for paleoceanographic reconstructions. As such, this study constrains modern depth habitats for the northern equatorial Indian Ocean, for 14 planktonic foraminiferal species (G. ruber, G. elongatus, G. pyramidalis, G. rubescens, T. sacculifer, G. siphonifera, G. glutinata, N. dutertrei, G. bulloides, G. ungulata, P. obliquiloculata, G. menardii, G. hexagonus, G. scitula) using stable isotopic signatures (δ¹⁸O and δ¹³C) and Mg/Ca ratios. We evaluate two aspects of inferred depth habitats: (1) the significance of the apparent calcification depth (ACD) calculation method/equations and (2) regional species-specific ACD controls. Through a comparison with five global, (sub)tropical studies we found the choice of applied equation and δ¹⁸O_sw significant and an important consideration when comparing with the published literature. The ACDs of the surface mixed layer and thermocline species show a tight clustering between 73–109 m water depth coinciding with the deep chlorophyll maximum (DCM). Furthermore, the ACDs for the sub-thermocline species are positioned relative to secondary peaks in the local primary production. We surmise that food source plays a key role in the relative living depths for the majority of the investigated planktonic foraminifera within this oligotrophic environment of the Maldives and elsewhere in the tropical oceans.

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea

The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO₂^-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.

Environmental conditions and neutral processes shape the skin microbiome of European catfish (Silurus glanis) populations of Southwestern France

Teleost fishes interact with diverse microbial communities, playing crucial functions for host fitness. While gut microbiome has been extensively studied, skin microbiome has been overlooked. Specifically, there is no assessment of the relative impact of host and environmental factors on microbiome variability as well as neutral processes shaping fish skin microbiome. Here, we assessed the skin microbiome of a Siluriforme, the European catfish (Silurus glanis) sampled in four sites located in Southwestern France. We assessed the relative roles of individual features (body size and genetic background), local environment and neutral processes in shaping skin microbiome. Catfish skin microbiome composition was distinct to that of other freshwater fish species previously studied with high abundances of Gammaproteobacteria and Bacteroidetes. We found no effect of catfish individual genotype and body size on the structure of its associated skin microbiome. Geographical location was the best catfish skin microbiome structure predictor, together with neutral models of microbiome assembly.

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.

Culture dependent and independent analysis and appraisal of early stage biofilm-forming bacterial community composition in the Southern coastal seawater of India

Microbial aggregation on artificial surfaces is a fundamental phenomenon in aquatic systems that lead to biofouling, corrosion and influence the buoyancy of plastic materials. Despite the maritime activities and with nearshore large industrial sector, Laccadive Sea in the Indian Ocean has rarely been investigated for characterizing early biofilm-forming bacterial community. The present investigation was aimed to catalogue the primary colonizers on artificial surfaces and their comparison with planktonic community in southern coastal seawater of India. Surface seawater samples and biofilm assembled on three artificial surfaces over a period of 72 h of immersion in the intake area of a nuclear power plant at Kudankulam, India were collected. The structure of surface assemblages and plankton were unveiled by employing culture dependent, DGGE and NGS methods. In static condition, a collection of aerobic heterotrophic bacteria was screened in vitro for their ability to form potent biofilm. Proteobacteria preponderated the communities both in seawater and natural biofilm and Gammaproteobacteria accounted for >85% in the latter. Vibrionaceae, Alteromonadaceae and Pseudoalteromonadaceae dominated the biofilm community and constituted for 41, 25 and 8%, respectively. In contrast to other studies that showed Rhodobacteraceae family of Alphaproteobacteria as predominant component, we found Vibrionaceae of Gammaproteobacteria as dominant group in early stage of biofilm formation. Both DGGE and NGS data indicated that the attached community is noticeably distinct from those suspended in water column and form the basis for the proposed hypothesis of species sorting theory, that is, the local environmental conditions influence bacterial community assembly. Collectively, the data are testament for species sorting process that occur during initial assembly of bacterial community in marine environment and shed light on the structure of marine bacterial biofilm development. The outcome of the present study is of immense importance for designing long-term, efficient and appropriate strategies to control the biofouling phenomenon.

Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species

Most research on extant planktonic foraminifera has been directed towards larger species (>0.150 mm) which can be easily manipulated, counted and yield enough calcite for geochemical analyses. This has drawn attention towards the macroperforate clade and created an impression of their numerical and ecological dominance. Drawing such conclusions from the study of such “giants” is a dangerous path. There were times in the evolutionary history of planktonic foraminifera when all species were smaller than 0.1 mm and indeed numerous small taxa, mainly from the microperforate clade, have been formally described from the modern plankton. The significance of these small, obscure and neglected species is poorly characterized and their relationship to the newly discovered hyperabundant but uncharacterized lineages of planktonic foraminifera in metabarcoding datasets is unknown. To determine, who is hiding in the metabarcoding datasets, we carried out an extensive sequencing of 18S rDNA targeted at small and obscure species. The sequences of the newly characterized small and obscure taxa match many of the previously uncharacterized lineages found in metabarcoding data. This indicates that most of the modern diversity in planktonic foraminifera has been taxonomically captured, but the role of the small and neglected taxa has been severely underestimated.

Stratification, nitrogen fixation, and cyanobacterial bloom stage regulate the planktonic food web structure

Changes in the complexity of planktonic food webs may be expected in future aquatic systems due to increases in sea surface temperature and an enhanced stratification of the water column. Under these conditions, the growth of unpalatable, filamentous, N₂ -fixing cyanobacterial blooms, and their effect on planktonic food webs will become increasingly important. The planktonic food web structure in aquatic ecosystems at times of filamentous cyanobacterial blooms is currently unresolved, with discordant lines of evidence suggesting that herbivores dominate the mesozooplankton or that mesozooplankton organisms are mainly carnivorous. Here, we use a set of proxies derived from amino acid nitrogen stable isotopes from two mesozooplankton size fractions to identify changes in the nitrogen source and the planktonic food web structure across different microplankton communities. A transition from herbivory to carnivory in mesozooplankton between more eutrophic, near-coastal sites and more oligotrophic, offshore sites was accompanied by an increasing diversity of microplankton communities with aging filamentous cyanobacterial blooms. Our analyses of 124 biotic and abiotic variables using multivariate statistics confirmed salinity as a major driver for the biomass distribution of non-N₂ -fixing microplankton species such as dinoflagellates. However, we provide strong evidence that stratification, N₂ fixation, and the stage of the cyanobacterial blooms regulated much of the microplankton diversity and the mean trophic position and size of the metabolic nitrogen pool in mesozooplankton. Our empirical, macroscale data set consistently unifies contrasting results of the dominant feeding mode in mesozooplankton during blooms of unpalatable, filamentous, N₂ -fixing cyanobacteria by identifying the at times important role of heterotrophic microbial food webs. Thus, carnivory, rather than herbivory, dominates in mesozooplankton during aging and decaying cyanobacterial blooms with hitherto uncharacterized consequences for the biogeochemical functions of mesozooplankton.

The Impact of Anthropogenic Disturbance on Bacterioplankton Communities During the Construction of Donghu Tunnel (Wuhan, China)

Bacterioplankton are both primary producers and primary consumers in aquatic ecosystems, which were commonly investigated to reflect environmental changes, evaluate primary productivity, and assess biogeochemical cycles. However, there is relatively less understanding of their responses to anthropogenic disturbances such as constructions of dams/tunnels/roads that may significantly affect the aquatic ecosystem. To fill such gap, this study focused on the bacterioplankton communities' diversity and turnover during a tunnel construction across an urban lake (Lake Donghu, Wuhan, China), and five batches of samples were collected within 2 months according to the tunnel construction progress. Results indicated that both resources and predator factors contributed significant to the variations of bacterioplankton communities, but the closed area and open areas showed different diversity patterns due to the impacts of tunnel construction. Briefly, the phytoplankton, TN, and TP in water were still significantly correlated with the bacterioplankton composition and diversity like that in normal conditions. Additionally, the organic matter, TN, and NH₄-N in sediments also showed clear effects on the bacterioplankton. However, the predator effects on the bacterioplankton in the closed-off construction area mainly derived from large zooplankton (i.e., cladocerans), while small zooplankton such as protozoa and rotifers are only responsible for weak predator effects on the bacterioplankton in the open areas. Further analysis about the ecological driving forces indicated that the bacterioplankton communities' turnover during the tunnel construction was mainly governed by the homogeneous selection due to similar environments within the closed area or the open areas at two different stages. This finding suggests that bacterioplankton communities can quickly adapt to the environmental modifications resulting from tunnel construction activities. This study can also give references to enhance our understanding on bacterioplankton communities' response to ecological and environmental changes due to intensification of construction and urbanization in and around lake ecosystems.

Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae

The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes. However, 18S reference barcodes for this important family are still relatively scarce. We provide 18S rDNA and partial 28S rDNA reference sequences of 443 morphologically characterized chaetocerotacean strains. We gathered 164 of the 216 18S sequences and 244 of the 413 28S sequences of strains from the Gulf of Naples, Atlantic France, and Chile. Inferred phylogenies showed 84 terminal taxa in seven principal clades. Two of these clades included terminal taxa whose rDNA sequences contained spliceosomal and Group IC1 introns. Regarding the commonly used metabarcode markers in planktonic diversity studies, all terminal taxa can be discriminated with the 18S V4 hypervariable region; its primers fit their targets in all but two species, and the V4-tree topology is similar to that of the 18S. Hence V4-metabarcodes of unknown Chaetocerotaceae are assignable to the family. Regarding the V9 hypervariable region, most terminal taxa can be discriminated, but several contain introns in their primer targets. Moreover, poor phylogenetic resolution of the V9 region affects placement of metabarcodes of putative but unknown chaetocerotacean taxa, and hence, uncertainty in taxonomic assignment, even of higher taxa.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Plankton community assessment in anthropogenic-impacted oligotrophic coastal regions

Microbial planktonic communities are critical components of marine biogeochemical pathways. Despite this, there is still limited knowledge on the dynamics of this group in warm and oligotrophic waters. We used high-throughput sequencing to characterise the bacterial (16S rRNA) and eukaryotic (18S rRNA) microbial plankton communities in two regions under the influence of anthropogenic impacts (a port and sewage outflow) and a coastal region with no direct anthropogenic disturbances in the central Red Sea. Overall, bacterial and eukaryotic components responded in a similar way to the environmental conditions. Community composition and structure were more sensitive than alpha diversity measures to environmental impacts. With the exception of eukaryotes, for which the number of OTU differed significantly between sampling periods in all the regions, environmental changes associated with anthropogenic pressures seem to be better reflected by variations in the relative dominance of microbial groups. For example, elevated proportional abundances of nitrifying and sewage-/faecal-related bacteria at the impacted sites were observed compared with the coastal region. The recently developed microgAMBI also appeared to correlate well with the level of anthropogenic impact the regions experienced, showing the potential to be applied in oligotrophic waters.

Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011)

The unique macroevolutionary dataset of Aze & others has been transferred onto the TimeScale Creator visualisation platform while, as much as practicable, preserving the original unrevised content of its morphospecies and lineage evolutionary trees. This is a "Corrected Version" (not a revision), which can serve as an on-going historical case example because it is now updatable with future time scales. Both macroevolutionary and biostratigraphic communities are now equipped with an enduring phylogenetic database of Cenozoic macroperforate planktonic foraminiferal morphospecies and lineages for which both graphics and content can be visualised together. Key to maintaining the currency of the trees has been specification of time scales for sources of stratigraphic ranges; these scales then locate the range dates within the calibration series. Some ranges or their sources have undergone mostly minor corrections or amendments. Links between lineage and morphospecies trees have been introduced to improve consistency and transparency in timing within the trees. Also, Aze & others' dual employment of morphospecies and lineage concepts is further elaborated here, given misunderstandings that have ensued. Features displayed on the trees include options for line styles for additional categories for range extensions or degrees of support for ancestor-descendant proposals; these have been applied to a small number of instances as an encouragement to capture more nuanced data in the future. In addition to labeling of eco- and morpho-groups on both trees, genus labels can be attached to the morphospecies tree to warn of polyphyletic morphogenera, and the lineage codes have been decoded to ease their recognition. However, it is the mouse-over pop-ups that provide the greatest opportunity to embed supporting information in the trees. They include details for stratigraphic ranges and their recalibration steps, positions relative to the standard planktonic-foraminiferal zonation, and applications as datums, as well as mutual listings between morphospecies and lineages which ease the tracing of their interrelated contents. The elaboration of the original dataset has been captured in a relational database, which can be considered a resource in itself, and, through queries and programming, serves to generate the TimeScale Creator datapacks.

Microplankton dynamics of a coastal lagoon, Chilika: interactive effect of environmental parameters on microplankton groups

Microplankton population of Asia's largest coastal lagoon Chilika was studied for five major groups, bacillariophyceae, cyanophyceae, chlorophyceae, dinophyceae, rotifera, and tintinninae. The study reported presence of 233 species of microplankton whose average annual abundance was 1631 cells/l. The physicochemical parameters contributing to the spatio-temporal fluctuations in microplankton diversity, abundance, and community structure were identified as salinity, pH, DO, nitrate, and silicate. Salinity, transparency, depth, and silicate most explained the abundance of bacillariophyceae; nitrate, pH, and DO influenced cyanophyceae; salinity, transparency, and chlorophyll concentration influenced chlorophyceae; salinity, depth, and water temperature influenced dinophyceae; salinity, free CO2, and nitrate-influenced rotifers, whereas salinity, pH, DO, and depth influenced tintinnids. Biotic-abiotic relationships revealed particular preference of environmental conditions at species level in groups like bacillariophyceae, cyanophyceae, and dinophyceae. Although the lagoon is shallow, bacillariophyceae-environment interaction showed depth can be a critical factor for species like Aulocoseira sp., Amphipleura sp., and Rhophalodia sp. Species of dinoflagellates like Dinophysis caudata, Noctiluca scintillans, and Protoperidinium proliferated in lower level of silicate. Unlike other cyanophyceae species Streptococcus sp., Chroococcus sp., Diplococcus sp., Aphanocapsa sp., and Gloeocapsa sp. were negatively influenced by nitrate concentration. The study provides better scope for ecological management of the lagoon with respect to conserving biodiversity and hydrological quality of the ecosystem.

Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi

BACKGROUND

Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.

RESULTS

Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.

CONCLUSIONS

Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

Short timescale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rRNA gene) and rRNA molecules (rRNA) of Bacteria, Archaea, and Eukaryota once to twice daily between March 2014 and May 2014 from the surface ocean off Catalina Island, California. Typically Ostreococcus, Braarudosphaera, Teleaulax, and Synechococcus dominated phytoplankton sequences (including chloroplasts) while SAR11, Sulfitobacter, and Fluviicola dominated non-phytoplankton Bacteria and Archaea. We observed short-lived increases of diatoms, mostly Pseudo-nitzschia and Chaetoceros, with quickly responding Bacteria and Archaea including Flavobacteriaceae (Polaribacter & Formosa), Roseovarius, and Euryarchaeota (MGII), notably the exact amplicon sequence variants we observed responding similarly to another diatom bloom nearby, 3 years prior. We observed correlations representing known interactions among abundant phytoplankton rRNA sequences, demonstrating the biogeochemical and ecological relevance of such interactions: (1) The kleptochloroplastidic ciliate Mesodinium 18S rRNA gene sequences and a single Teleaulax taxon (via 16S rRNA gene sequences) were correlated (Spearman r = 0.83) yet uncorrelated to a Teleaulax 18S rRNA gene OTU, or any other taxon (consistent with a kleptochloroplastidic or karyokleptic relationship) and (2) the photosynthetic prymnesiophyte Braarudosphaera bigelowii and two strains of diazotrophic cyanobacterium UCYN-A were correlated and each taxon was also correlated to other taxa, including B. bigelowii to a verrucomicrobium and a dictyochophyte phytoplankter (all r > 0.8). We also report strong correlations (r > 0.7) between various ciliates, bacteria, and phytoplankton, suggesting interactions via currently unknown mechanisms. These data reiterate the utility of high-frequency time series to show rapid microbial reactions to stimuli, and provide new information about in situ dynamics of previously recognized and hypothesized interactions.

Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa. Furthermore, the environmental (selective processes) and spatial (neutral processes) factors seemed to govern the assembly and biogeography of abundant and rare bacterial subcommunities, although both factors explained only a small fraction of variation within the rare subcommunity. More importantly, variation partitioning (based on adjusted R2 in redundancy analysis) showed that spatial factors exhibited a slightly greater influence on both abundant and rare subcommunities compared to environmental selection; however, the abundant subcommunity had a much stronger response to spatial factors (17.3% of pure variance was explained) than that shown by the rare bacteria (3.5%). These results demonstrate that environmental selection and neutral processes explained the similar biogeographic patterns of abundant and rare subcommunities, but a large proportion of unexplained variation in the rare taxa (91.1%) implies that more complex assembly mechanisms may exist to shape the rare bacterial assemblages in the three subtropical bays.

Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community

Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.

Taxonomical Resolution and Distribution of Bacterioplankton Along the Vertical Gradient Reveals Pronounced Spatiotemporal Patterns in Contrasted Temperate Freshwater Lakes

We examined the relationship between viruses and co-occurring bacterial communities across spatiotemporal scale in two contrasting freshwater lakes, namely meromictic Lake Pavin and dimictic Lake Aydat (Central France). Next-generation sequencing of 16S rRNA genes suggested distinct patterns in bacterioplankton community composition (BCC) between the lakes over depths and seasons. BCC were generally dominated by members of Actinobacteria, Proteobacteria, and Bacteroidetes covering about 95% of all sequences. Oxygen depletion at the bottom waters in Aydat and existence of permanent anoxia in the monimolimnion of Pavin resulted in the occurrence and dominance of lesser known members of lake communities such as Methylotenera, Methylobacter, Gallionella, Sulfurimonas, and Syntrophus in Pavin and Methylotenera and Sulfuritalea in Aydat. Differences in BCC appeared strongly related to dissolved oxygen concentration, temperature, viral infection, and virus-to-bacteria ratio. UniFrac analysis indicated a clear distinction in BCC when the percentage of viral infected bacterial cells and virus-to-bacteria ratio exceeded a threshold level of 10% and 5, respectively, suggesting a link between viruses and their potential bacterial host communities. Our study revealed that in both the lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.

Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river

Although the influence of microbial community assembly processes on aquatic ecosystem function and biodiversity is well known, the processes that govern planktonic communities in human-impacted rivers remain largely unstudied. Here, we used multivariate statistics and a null model approach to test the hypothesis that environmental conditions and obstructed dispersal opportunities, dictate a deterministic community assembly for phytoplankton and bacterioplankton across contrasting hydrographic conditions in a subtropical mid-sized river (Jiulong River, southeast China). Variation partitioning analysis showed that the explanatory power of local environmental variables was larger than that of the spatial variables for both plankton communities during the dry season. During the wet season, phytoplankton community variation was mainly explained by local environmental variables, whereas the variance in bacterioplankton was explained by both environmental and spatial predictors. The null model based on Raup-Crick coefficients for both planktonic groups suggested little evidences of the stochastic processes involving dispersal and random distribution. Our results showed that hydrological change and landscape structure act together to cause divergence in communities along the river channel, thereby dictating a deterministic assembly and that selection exceeds dispersal limitation during the dry season. Therefore, to protect the ecological integrity of human-impacted rivers, watershed managers should not only consider local environmental conditions but also dispersal routes to account for the effect of regional species pool on local communities.

Distinctive Patterns in the Taxonomical Resolution of Bacterioplankton in the Sediment and Pore Waters of Contrasted Freshwater Lakes

Bacteria assemblages in lake sediments play a key role in various biogeochemical processes, yet their association with interstitial pore waters has been scarcely investigated. In this study, we utilized Illumina next-generation amplicon sequencing of the 16S rRNA gene to characterize the seasonal bacterial communities in the sediments and pore waters of three contrasted temperate freshwater lakes, namely Pavin, Aydat, and Grangent (French Massif Central). Despite occupying seemingly similar habitats, bacterial communities differed substantially between sediments and pore waters at all seasons with low sharing of operational taxonomic units (OTUs, 6.7 to 20.3%) between them. Sediment-associated bacteria were more rich and diverse than pore water bacteria, indicating a high heterogeneity in the sediment microhabitat. The changes in both sediment and pore water bacterial communities were lake and season specific. The bacterial community showed distinct differences between the lakes, with larger presence of strict anaerobes such as Syntrophus, Syntrophorhabdus, and Sulfuricurvum in the pore water and sediments of Pavin responsible for carbon and sulfur cycling. In both Aydat and Grangent, the hgcI_clade dominated throughout the study period in the pore waters. The higher representation of lesser-known transient members of lake communities such as Methylotenera in the pore waters of Aydat, and Clostridium and Sulfuricurvum in the pore and sediments of Grangent, respectively, were observed during the period of temporary anoxia in summer caused by lake stratification. Our study revealed that in the investigated lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.

Community Composition and Diversity of Coastal Bacterioplankton Assemblages in Lakes Michigan, Erie, and Huron

The Laurentian Great Lakes, including Lakes Superior, Michigan, Huron, Erie, and Ontario, located in the eastern part of North America are considered the largest of freshwater lakes in the world; however, very little is known about the diversity and distribution of indigenous microbial assemblages within these vast bodies of freshwater systems. Therefore, to delineate the microbial structure and community composition in these aquatic environments, combinations of high-throughput sequencing and fluorescent in situ hybridization (FISH) approaches were utilized to quantitatively characterize the occurrence, diversity, and distribution of bacterioplankton assemblages in six different sites located along the coastal regions of Lakes Michigan, Huron, and Erie. Phylogenetic examination showed a diverse bacterial community belonging to 11 different taxonomic groups. Pyrosequencing results revealed that the majority of the sequences were clustered into four main groups, i.e., Proteobacteria, Bacteriodetes, Actinobacteria, and Cyanobacteria, while fluorescent in situ hybridization also showed the numerical dominance of members of the Gammaproteobacteria and the Cytophaga-Flavobacterium in the six lake sites examined. Overall, the assemblages were shown to be quite diverse in distribution among the lake sites examined, comprising mostly of various heterotrophic populations, with the exception of the Lake Erie-Sandusky Bay site with more than 50% domination by autotrophic Cyanobacteria. This indicates that combinations of factors including water chemistry and various anthropogenic disturbances as well as the lake morphometric characteristics are probably influencing the community structure and diversity of the bacterial assemblages within the systems.

Are oceanic fronts ecotones? Seasonal changes along the subtropical front show fronts as bacterioplankton transition zones but not diversity hotspots

Ecotones are regarded as diversity hotspots in terrestrial systems, but it is unknown if this 'ecotone effect' occurs in the marine environment. Oceanic fronts are widespread mesoscale features, present in the boundary between different water masses, and are arguably the best potential examples of ecotones in the ocean. Here we performed the first seasonal study along an oceanic front, combining 16S rRNA gene sequencing coupled with a high spatial resolution analysis of the physical properties of the water masses. Using the Subtropical Frontal Zone off New Zealand we demonstrate that fronts delimit shifts in bacterioplankton community composition between water masses, but that the strength of this effect is seasonally dependent. While creating a transition zone where physicochemical parameters and bacterioplankton communities get mixed, this ecotone does not result in increased diversity. Thus unlike terrestrial ecotones, oceanic fronts are boundaries but not hotspots of bacterioplankton diversity in the ocean.

A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog

Devils Hole is the sole natural habitat of the critically endangered Devils Hole pupfish (Cyprinodon diabolis). To establish a backup population, the Ash Meadows Fish Conservation Facility (AMFCF), a full-scale replica of the uppermost 6.7 m of Devils Hole, was constructed by management agencies in the mid-2010s. Despite rigorous efforts to mimic the bathymetric and physical details of the Devils Hole environment, the biogeochemistry and microbiology of the AMFCF refuge tank remain largely unaddressed. We evaluated water physicochemistry and employed Illumina DNA sequencing of 16S rRNA gene libraries to evaluate planktonic and benthic bacterial and archaeal community composition within their respective physicochemical contexts in Devils Hole and AMFCF on the same day. Major ion concentrations were consistent between the two systems, but water temperature and dissolved oxygen dynamics differed. Bioavailable nitrogen (primarily nitrate) was 5x lower in AMFCF. Devils Hole and AMFCF nitrogen:phosphorus molar ratios were 107:1 and 22:1, indicative of different nutrient control mechanisms. Both sites are microbiologically diverse, with over 40 prokaryotic phyla represented at each, with 37 shared between them and nearly than half deriving from candidate divisions. The abundance and composition of predicted photosynthetic primary producers (Cyanobacteria) was markedly different between sites: Devils Hole planktonic and sediment communities were dominated by Oscillatoria spp. (13.2% mean relative abundance), which proved virtually undetectable in AMFCF. Conversely, AMFCF was dominated by a predicted heterotroph from the Verrucomicrobiaceae family (31.7%); which was comparatively rare (<2.4%) in Devils Hole. We propose that the paucity of bioavailable nitrogen in AMFCF, perhaps resulting from physical isolation from allochthonous environmental inputs, is reflected in the microbial assemblage disparity, influences biogeochemical cycling of other dissolved constituents, and may ultimately impact survivorship and recruitment of refuge populations of the Devils Hole pupfish.

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons

Viruses are the most abundant components of microbial food webs and play important ecological and biogeochemical roles in aquatic ecosystems. Virioplankton is regulated by several environmental factors, such as salinity, turbidity, and humic substances. However, most of the studies aimed to investigate virioplankton regulation were conducted in temperate systems combining a limited range of environmental variables. In this study, virus abundance and production were determined and their relation to bacterial and limnological variables was assessed in 20 neighboring shallow tropical coastal lagoons that present wide environmental gradients of turbidity (2.32-571 NTU), water color (1.82-92.49 m^-1), dissolved organic carbon (0.71-16.7 mM), salinity (0.13-332.1‰), and chlorophyll-a (0.28 to 134.5 μg L^-1). Virus abundance varied from 0.37 × 10⁸ to 117 × 10⁸ virus-like-particle (VLP) mL^-1, with the highest values observed in highly salty aquatic systems. Salinity and heterotrophic bacterial abundance were the main variables positively driving viral abundances in these lagoons. We suggest that, with increased salinity, there is a decrease in the protozoan control on bacterial populations and lower bacterial diversity (higher encounter rates with virus specific hosts), both factors positively affecting virus abundance. Virus production varied from 0.68 × 10⁷ to 56.5 × 10⁷ VLP mL^-1 h^-1 and was regulated by bacterial production and total phosphorus, but it was not directly affected by salinity. The uncoupling between virus abundance and virus production supports that the hypothesis that the lack of grazing pressure on viral and bacterial populations is an important mechanism causing virus abundance to escalate with increasing salt concentrations.

Variability of ultraplankton composition and distribution in an oligotrophic coastal ecosystem of the NW Mediterranean Sea derived from a two-year survey at the single cell level

Ultraplankton [heterotrophic prokaryotes and ultraphytoplankton (<10 μm)] were monitored weekly over two years (2009 & 2010) in a coastal area of the NW Mediterranean Sea. Six clusters were differentiated by flow cytometry on the basis of their optical properties, two heterotrophic prokaryote (HP) subgroups labelled LNA and HNA (low and high nucleic acid content respectively), Prochlorococcus, Synechococcus, autotrophic picoeukaryotes and nanoeukaryotes. HP represented an important component of the microbial assemblage over the survey with relatively small abundance variation through seasons. The carbon biomass ratio HP/ultraphytoplankton averaged 0.45, however this ratio exceeded 1 during spring. Ultraphytoplankton biomass made about 50% of the total autotrophic carbon estimates but this contribution increased up to 97% and 67% during the 2009 and 2010 spring periods respectively. Within ultraphytoplankton, nanoeukaryote represent the most important ultraphytoplankton group in terms of autotrophic carbon biomass (up to 70%). Picoeukaryote maximum abundance occurred in winter. Synechococcus was the most abundant population (maximum 1.2 x 10 5 cells cm-3) particularly in spring where it represented up to 54% of ultraphytoplankton carbon biomass. The warmer winter-spring temperatures and the lengthening of the stratification period created a favorable situation for the earlier appearance of Synechococcus and its persistence throughout summer, paralleling Prochlorococcus development. Prochlorococcus was dominant over summer and autumn with concentrations up to 1.0 × 10 5 cells cm-3. While the abundance of Synechococcus throughout survey was of the same order as that reported in western Mediterranean Sea, Prochlorococcus was more abundant and similar to the more typical oligotrophic and warm waters. The abundance variation of the ultraplankton components through the survey was relatable to variations in the hydrological and nutrient conditions.

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

The oxygenated hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that the communities in the oxygenated hypolimnia were distinct from those in the epilimnia and identified several predominant lineages inhabiting multiple lakes. Catalyzed reporter deposition fluorescence in situ hybridization revealed that abundant hypolimnion-specific lineages, CL500-11 (Chloroflexi), CL500-3, CL500-37, CL500-15 (Planctomycetes) and Marine Group I (Thaumarchaeota), together accounted for 1.5-32.9% of all bacterioplankton in the hypolimnion of the lakes. Furthermore, an analysis of single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of different sub-populations between lakes and water layers among the lineages occurring in the entire water layer (for example, acI-B1 and acI-A7). Collectively, these results provide the first comprehensive overview of the bacterioplankton community in the oxygenated hypolimnion of deep freshwater lakes.

Biodegradation and Detoxification of Sanitary Landfill Leachate by Stabilization Ponds System

  The performance of a pilot stabilization ponds system was evaluated for the treatment of sanitary landfill leachate, focusing on effluent detoxification. Three serial ponds (anaerobic-P1, facultative-P2, and maturation-P3) were evaluated during two different operational conditions: natural condition (period 1) and 24 hours of artificial aeration in P2 (period 2). The ponds system exhibited removal efficiencies of 53% for soluble chemical oxygen demand (SCOD), 81% for filtered biochemical oxygen demand (FBOD), and 84% for NH4+-N during period 1 and 70% for SCOD, 80% for FBOD, and 96% for <inline-graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="00539-ilm01.gif"/>-N during period 2. Most metals (Fe, Cu, Cd, Zn, Cr, Ni, and Pb) and organic compounds in the leachate were significantly reduced in the treatment system, with greater reductions during period 2. Moreover, toxicity tests demonstrated the capacity of the system to reduce the toxicity of the raw leachate (up to 89% toxicity reduction).

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups

Heterotrophic flagellates contribute significantly to the matter flux in aquatic and terrestrial ecosystems. Still today their quantification and taxonomic classification bear several problems in field studies, though these methodological problems seem to be increasingly ignored in current ecological studies. Here we describe and test different methods, the live-counting technique, different fixation techniques, cultivation methods like the liquid aliquot method (LAM), and a molecular single cell survey called aliquot PCR (aPCR). All these methods have been tested either using aquatic field samples or cultures of freshwater and marine taxa. Each of the described methods has its advantages and disadvantages, which have to be considered in every single case. With the live-counting technique a detection of living cells up to morphospecies level is possible. Fixation of cells and staining methods are advantageous due to the possible long-term storage and observation of samples. Cultivation methods (LAM) offer the possibility of subsequent molecular analyses, and aPCR tools might complete the deficiency of LAM in terms of the missing detection of non-cultivable flagellates. In summary, we propose a combination of several investigation techniques reducing the gap between the different methodological problems.