Genetic diversity along the life cycle of the cyanobacterium Microcystis: highlight on the complexity of benthic and planktonic interactions

Microcystis is a toxic freshwater cyanobacterium with an annual life cycle characterized by the alternation of a planktonic proliferation stage in summer and a benthic resting stage in winter. Given the importance of both stages for the development and the survival of the population, we investigated the genotypic composition of the planktonic and benthic Microcystis subpopulations from the Grangent reservoir (France) during two distinct proliferation periods. Our results showed a succession of different dominant genotypes in the sediment as well as in the water all along the study periods with some common genotypes to both compartments. Analysis of molecular variance and UniFrac analysis confirmed the similarity between some benthic and planktonic samples, thus evidencing exchanges of genotypes between water and sediment. Thanks to these data, recruitment and sedimentation were proven not to be restricted to spring and autumn, contrary to what was previously thought. Finally, genetic diversity was significantly higher in the sediment than in the water (P < 0.01; Student's t‐test). Taken together, our results shed light on the hidden contribution of the benthic compartment in maintaining the genetic diversity of Microcystis populations throughout their annual cycle, which could explain their ecological success in aquatic ecosystems.     

Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary

Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.     

Coastal marine habitats harbor novel early-diverging fungal diversity

Despite nearly a century of study, the diversity of marine fungi remains poorly understood. Historical surveys utilizing microscopy or culture-dependent methods suggest that marine fungi are relatively species-poor, predominantly Dikarya, and localized to coastal habitats. However, the use of high-throughput sequencing technologies to characterize microbial communities has challenged traditional concepts of fungal diversity by revealing novel phylotypes from both terrestrial and aquatic habitats. Here, I used ion semiconductor sequencing (Ion Torrent) of the ribosomal large subunit (LSU/28S) to explore fungal diversity from water and sediment samples collected from four habitats in coastal North Carolina. The dominant taxa observed were Ascomycota and Chytridiomycota, though all fungal phyla were represented. Diversity was highest in sand flats and wetland sediments, though benthic sediments harbored the highest proportion of novel sequences. Most sequences assigned to early-diverging fungal groups could not be assigned beyond phylum with statistical support, suggesting they belong to unknown lineages.     

Planktonic and sediment bacterial communities in an integrated mariculture system

An integrated multi-trophic aquaculture (IMTA) system, with one fish cage model surrounded by an island and shellfish rafts, was used in the current study. Planktonic and sediment bacterial communities in the IMTA system were monitored over four seasons in 2019. In both plankton and sediment samples, the most dominant phyla were Proteobacteria and Bacteroidota. Sediment bacterial samples were more similar and had higher levels of biodiversity than planktonic bacterial samples. Obvious seasonal variations were found in plankton samples, but not in sediment samples. No obvious inter-site variations in planktonic and sediment bacteria (fish cages, shellfish rafts and control sites) were found and the results suggested that no obvious impact of feeding operations in fish culture cage model on bacterial communities in the IMTA system was observed in this study. Based on the sequence data, some faecal indicator bacteria and potentially pathogenic bacterial species were detected. According to the results, the bacterial water quality in the IMTA system was acceptable. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis revealed that the primary difference in potential functional roles of planktonic and sediment bacteria was amino acid transport and metabolism, which was active in different seasons.     

Highlighting patterns of fungal diversity and composition shaped by ocean currents using the East China Sea as a model

How ocean currents shape fungal transport, dispersal and more broadly fungal biogeography remains poorly understood. The East China Sea (ECS) is a complex and dynamic habitat with different water masses blending microbial communities. The internal transcribed spacer 2 region of fungal rDNA was analysed in water and sediment samples directly collected from the coastal (CWM), Kuroshio (KSWM), Taiwan warm (TWM) and the shelf mixed water mass (MWM), coupled with hydrographic properties measurements, to determine how ocean currents impact the fungal community composition. Almost 9k fungal operational taxonomic units (OTUs) spanning six phyla, 25 known classes, 102 orders and 694 genera were obtained. The typical terrestrial and freshwater fungal genus, Byssochlamys, was dominant in the CWM, while increasing abundance of a specific OTU affiliated with Aspergillus was revealed from coastal to open ocean water masses (TWM and KSWM). Compared with water samples, sediment harboured an increased diversity with distinct fungal communities. The proximity of the Yangtze and Qiantang estuaries homogenizes the surface water and sediment communities. A significant influence of ocean currents on community structure was found, which is believed to reduce proportionally the variation explained by environmental parameters at the scale of the total water masses. Dissolved oxygen and depth were identified as the major parameters structuring the fungal community. Our results indicate that passive fungal dispersal driven by ocean currents and river run‐off, in conjunction with the distinct hydrographic conditions of individual water masses, shapes the fungal community composition and distribution pattern in the ECS.     

The inshore marine ecosystem off the Vestfold Hills,Antarctica

The planktonic, ice/water interface, and benthic communities at three sites off the coast of the Vestfold Hills, Antarctica, were examined over a complete year.The planktonic flora and fauna were composed predominantly of oceanic species with diatoms and copepods the numerically dominant groups. Primary production was largely restricted to the summer months except for epontic algae which developed in spring. The zooplankton exhibited a similar seasonal cycle but lagged some months behind that of the phytoplankton.The ice/water interface (epontic) fauna consisted of species from the plankton and benthos. Copepods were major contributors; however, two amphipod species dominated. Seasonality of the fauna in this habitat was determined by ice formation and breakout, and development of ice algae.Each of the benthic substrates supported a characteristic macrofaunal assemblage, although infaunal amphipods and tanaids were similar at each site. Infauna exhibited a distinct seasonal cycle related to that of the primary producers whereas macrofauna showed no seasonal changes in abundance.Species composition of each community in this coastal antarctic region was comparable with that of similar habitats in other antarctic coastal areas, supporting the circumpolarity of antarctic marine communities.     

鄱阳湖湖泊细菌群落组成及结构——以松门山为例

于2011年5月在鄱阳湖——松门山湖区采集底泥与表层水样,分别提取了表层水体浮游和底泥微生物基因组DNA,利用454高通量测序技术对细菌的16S rRNA基因进行了序列测定,分析了湖泊底泥细菌、水体浮游细菌群落结构特征。结果显示:底泥细菌OTUs(Operational Taxonomic Units)为1454,表层水体浮游细菌OTUs为269;底泥细菌群落比表层水体更加多样化,底泥细菌的物种数大大多于表层水体。同时,底泥细菌群落与表层浮游细菌群落结构存在显著差异。物种分类显示鄱阳湖底泥细菌种类隶属于20门,228属,其中优势种群为δ-变形菌纲(Deltaproteobacteria)、β-变形菌纲(Betaproteobacteria)和疣微菌门(Verrucomicrobia);表层水体浮游细菌隶属于13门116属,优势种群为β-变形菌纲、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria)。结果进一步揭示,无论是浮游细菌群落还是沉积物细菌群落,优势细菌种群的基因型多样性更高。     

Primary consumers as bioindicator of nitrogen pollution in lake planktonic and benthic food webs

The increased nitrogen loading from anthropogenic sources has affected aquatic ecosystems and has cascaded through food webs worldwide. Therefore, the evaluation of ecological impacts of anthropogenic nitrogen has become increasingly important. In this paper, we investigated the effect of nutrient enrichment in the planktonic and benthic food webs of a hypereutrophic urban lake using stable nitrogen isotope analysis. The stable isotope mixing model revealed that zooplanktons rely mainly on planktonic nitrogen, and that Chironomus and Oligochaete rely mainly on benthic nitrogen. The stable nitrogen isotope signatures of seston and the sediment organic matter can be a sensitive indicator, because they are correlated with the nitrogen content of water and sediment. Furthermore, the relationships between the stable nitrogen isotope values of primary production and primary consumers indicate that polluted nitrogen has transferred through the planktonic and benthic food webs, respectively. For primary consumers, the stable nitrogen isotope values of zooplanktons were correlated to nitrogen concentrations of water, and the stable nitrogen values of Chironomus and Oligochaete were correlated to the nitrogen content of sediment, respectively. This finding indicates that these primary consumers can be used as promising bioindicators of the anthropogenic nitrogen input in planktonic and benthic food webs, respectively. Our results suggest that stable nitrogen isotope of primary consumers can act as bioindicators to detect the dispersal patterns of anthropogenic contamination and understand the incorporation into and movement of waste nitrogen in pelagic and benthic food chains.     

Seasonal and microhabitat influences on diatom assemblages and their representation in sediment traps and surface sediments from adjacent High Arctic lakes: Cape Bounty,Melville Island,Nunavut

The spatial (i.e. microhabitat) and temporal (i.e. seasonal) characteristics of diatom assemblages in adjacent High Arctic lakes were studied intensively June–August 2004. These baseline data are used to improve understanding of modern diatom community dynamics, as well to inform paleoenvironmental reconstructions. Diatoms were collected approximately weekly through the melt season from each principal benthic substrate (moss/macrophyte, rock scrapes, littoral sediment), plankton, and sediment traps, and were compared to the uppermost 0.5 cm of a surface core obtained from the deepest part of the lake where sediment cores are routinely collected. Water samples were collected concurrently with diatom samples to investigate species–environment relationships. The lakes share approximately half of their common taxa, the most abundant overall in both lakes being small Cyclotella species. Results of detrended correspondence analysis (DCA) indicate that the largest gradient in species turnover existed between benthic and planktonic communities in both lakes, and that sediment trap and the surface core top samples most closely resemble the planktonic assemblage, with an additional contribution from the lotic environment. Our results indicate clear micro-spatial controls on species assemblages and a degree of disconnection between the benthos and deep lake sediments that manifests as an under-representation of benthic taxa in deep lake surface sediments. These findings are particularly relevant in the context of interpreting the paleoenvironmental record and assessing ecosystem sensitivity to continued climate change.     

Connecting through space and time: catchment-scale distributions of bacteria in soil,stream water and sediment

Terrestrial and aquatic environments are linked through hydrological networks that transport abiotic components from upslope environments into aquatic ecosystems. However, our understanding of how bacteria are transported through these same networks is limited. Here, we applied 16S rRNA gene sequencing to over 500 soil, stream water and stream sediment samples collected within a native forest catchment to determine the extent to which bacterial communities in these habitats are connected. We provide evidence that while the bacterial communities in each habitat were significantly distinct from one another (PERMANOVA pairwise P < 0.001), the bacterial communities in soil and stream samples were weakly connected to each other when stream sediment sample locations were downhill of surface runoff flow paths. This pattern decreased with increasing distance between the soil and sediment samples. The connectivity between soil and stream water samples was less apparent and extremely transient; the greatest similarity between bacterial communities in soil and stream water overall was when comparing stream samples collected 1 week post soil sampling. This study shows how bacterial communities in soil, stream water and stream sediments are connected at small spatial scales and provides rare insights into the temporal dynamics of terrestrial and aquatic bacterial community connectivity.     

Ocean currents shape the microbiome of Arctic marine sediments

Prokaryote communities were investigated on the seasonally stratified Alaska Beaufort Shelf (ABS). Water and sediment directly underlying water with origin in the Arctic, Pacific or Atlantic oceans were analyzed by pyrosequencing and length heterogeneity-PCR in conjunction with physicochemical and geographic distance data to determine what features structure ABS microbiomes. Distinct bacterial communities were evident in all water masses. Alphaproteobacteria explained similarity in Arctic surface water and Pacific derived water. Deltaproteobacteria were abundant in Atlantic origin water and drove similarity among samples. Most archaeal sequences in water were related to unclassified marine Euryarchaeota. Sediment communities influenced by Pacific and Atlantic water were distinct from each other and pelagic communities. Firmicutes and Chloroflexi were abundant in sediment, although their distribution varied in Atlantic and Pacific influenced sites. Thermoprotei dominated archaea in Pacific influenced sediments and Methanomicrobia dominated in methane-containing Atlantic influenced sediments. Length heterogeneity-PCR data from this study were analyzed with data from methane-containing sediments in other regions. Pacific influenced ABS sediments clustered with Pacific sites from New Zealand and Chilean coastal margins. Atlantic influenced ABS sediments formed another distinct cluster. Density and salinity were significant structuring features on pelagic communities. Porosity co-varied with benthic community structure across sites and methane did not. This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane.     

Combining otolith chemistry and telemetry to assess diadromous migration in pinkeye mullet, <Emphasis Type="Italic">Trachystoma petardi</Emphasis> (Actinopterygii,Mugiliformes)

Little is currently known regarding microbial community structure, and the environmental factors influencing it, within the anchialine ecosystem, defined as near-shore, land-locked water bodies with subsurface connections to the ocean and groundwater aquifer. The Hawaiian Archipelago is home to numerous anchialine habitats, with some on the islands of Maui and Hawaii harboring unique, laminated orange cyanobacterial–bacterial crusts that independently assembled in relatively young basalt fields. Here, benthic and water column bacterial and micro-eukaryotic communities from nine anchialine habitats on Oahu, Maui, and Hawaii were surveyed using high-throughput amplicon sequencing of the V6 (Bacteria-specific) and V9 (Eukarya-biased) hypervariable regions of the 16S- and 18S-rDNA genes, respectively. While benthic communities from habitats with cyanobacterial–bacterial crusts were more similar to each other than to ones lacking it on the same island, each habitat had distinct benthic and water column microbial communities. Analyses of the survey data in the context of environmental factors identified salinity, site, aquifer, and watershed as having the highest explanatory power for the observed variation in microbial diversity and community structure, with lesser drivers being annual rainfall, longitude, ammonium, and dissolved organic carbon. Our results epitomize the abiotic and biotic uniqueness characteristic of individual habitats comprising the Hawaiian anchialine ecosystem.     

Water level fluctuations in Lake Baringo,Kenya, during the 19th and 20th centuries: Evidence from lake sediments

This article presents a fossil diatom-based, semi-quantitative reconstruction of water level fluctuations for Lake Baringo over the past 200 years as a consequence of climatic variations. A 285 cm long sediment core sample was collected using a Rod-Operated Single-drive Stationary Piston corer. Lake level was inferred using indices based on the proportion of planktonic to benthic diatom taxa (P/B ratio). The sediment archive presented distinct zones dominated by planktonic and benthic diatom flora. An initial transgression in the early 19th century was characterised as a shallow water environment dominated by planktonic Aulacoseira spp. This was a response to extreme drought during the late 18th to early 19th century. Mid-19th century was defined by a high lake stand. The late 19th to early 20th centuries experienced low water level following the widely documented aridity at the time. The mid-20th century was marked by a spectacular rise in water level that coincided with remarkably wet years during the early 1960s and late 1970s. The first decade of the 21st century witnessed widespread changes in water level. The proxy records show that lake ramping and drawdown over the years follow approximately 50-year climatic cycles.     

POST-PLEISTOCENE DIATOM SUCCESSION IN DOUGLAS LAKE,MICHIGAN1,2

Analysis of fossil diatom assemblages recovered from a 12.2 m core reveals a series of distinct floristic associations. The associations present are correlated with sediment type and reflect successive stages in the development of the lake. A basal red clay sediment contains a planktonic association characteristic of large, proglacial lakes. At 10.0 m core depth, sediment type changes to fine sand containing a higher abundance of benthic species indicating reduction of water depth at the deposition site. Marl sediments begin at 9.7 m and contain an association characteristic of a small, shallow, oligotrophic lake. At 8.8 m the marl sequence is interrupted by highly organic sediment containing a eutrophic plankton association. From 8.5 to 7.6 m the sediment type grades from marl to organic, apparently reduced sediments and diatom associations present contain successively higher percentages of planktonic species associated with eutrophic habitats. By the 7.6 m level a eutrophic plankton association, similar to the modern flora, is established and remains remarkably constant to the surface of the section.     

Paleoceanographic implications of smaller benthic and planktonic foraminifera from the Eocene Pazin Basin (Coastal Dinarides,Croatia)

Summary Smaller benthic and planktonic foraminifera from the clastic sediments of the Pazin Basin (Istria, Croatia) were studied in order to obtain more data about paleoceanographic conditions that existed in the Middle Eocene Dinaric foreland basin. The succession investigated corresponds to the Middle Eocene planktonic foraminiferal zones Globigerapsis kugleri/Morozovella aragonensis (P11), Morozovella lehneri (P12), and Globigerapsis beckmanni (P13). Benthic foraminiferal assemblages from the clastic succession are dominated by epifaunal trochospiral genera suggesting oligotrophic to mesotrophic conditions and moderately oxygenated bottom waters. Planktonic foraminiferal assemblages indicate mesotrophic to eutrophic conditions of the surface waters, with increased eutrophication in the upper part of the section. Water depth, based on the ratio between planktonic and epifaunal benthic foraminifera and on the recognized species of cosmopolitan benthic foraminifera, was estimated to have been between about 900 and 1200 m. The basin was elongated and open to marine currents on both sides allowing good circulation and ventilation of the bottom water.     

Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes

The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions.     

Power law relationships among hierarchical taxonomic categories in algae reveal a new paradox of the plankton

Aim In this continental‐scale study, the biodiversity of benthic and planktonic algal communities was explored. A recent analysis of extinct and extant tree communities by Enquist et al. (2002) showed that richness of higher taxa was a power function of species richness, invariant across temporal and spatial scales. Here we examined whether the relationships between algal richness at hierarchical taxonomic levels conform to power laws as seen for trees, and if these relationships differ between benthic and planktonic habitats. Location Streams from more than 50 major watersheds in the United States. Method A total of 3698 samples were collected from 1277 locations by the National Water‐Quality Assessment Program. Three types of stream habitat were sampled: richest targeted habitats, depositional targeted habitats, and phytoplankton. The relationships between taxonomic richness at the species level vs. all higher categories from genus to phylum across the three habitats were examined by ordinary least squares (OLS) regressions after ln‐transformation of all variables. The slopes, b, of these regressions represent the exponents of the power functions that scaled the richness of higher taxonomic levels (T) to species richness (S) in the form: T∝S^b. Results Algal richness at hierarchical taxonomic categories (genus to phylum) is a power function of species richness. The scaling exponent of this function, which captures the diversification of higher taxa, i.e. the rate of increase of their richness with the increase of species richness, is significantly different across environments. Main conclusions The differential algal diversification in the three studied habitats emphasizes the fundamental role of the environment in structuring the communities of simple organisms such as algae. The finding that the diversification of higher taxa is greater in the seemingly homogeneous planktonic environment, when compared to benthic habitats, encompassing an array of ecological niches, poses a new paradox of the plankton.     

Aquatic macroinvertebrate assemblages in mitigated and natural wetlands

Many wetlands have been constructed in West Virginia as mitigation for a variety of human disturbances, but no comprehensive evaluation on their success has been conducted. Macroinvertebrates are extremely valuable components of functioning wetland ecosystems. As such, benthic and water column invertebrate communities were chosen as surrogates for wetland function in the evaluation of 11 mitigation and 4 reference wetlands in West Virginia. Mitigation wetlands ranged in age from 4 to 21 years old. Overall familial richness, diversity, density and biomass were similar between mitigation and reference wetlands (p > 0.05). Within open water habitats, total benthic invertebrate density was higher in reference wetlands, but mass of common taxa from water column samples was higher in mitigation wetlands (p < 0.05) Planorbidae density from benthic samples in emergent habitats was higher in reference than mitigated wetlands. Benthic Oligochaeta density was higher across open water habitats in mitigation wetlands. All other benthic taxa were similar between wetland types. Among the most common water column orders, Isopoda density was higher in reference wetlands, but Physidae density was higher in mitigation wetlands. Within mitigation wetlands, emergent areas contained higher richness and diversity than open areas. These data indicate that mitigation and reference wetlands generally support similar invertebrate assemblages, especially among benthic populations. The few observed differences are likely attributable to differences in vegetative community composition and structure. Mitigation wetlands currently support abundant and productive invertebrate communities, and as such, provide quality habitat for wetland dependent wildlife species, especially waterbirds and anurans.     

The hypolimnetic protozoan plankton of a eutrophic lake

The seasonal distribution of benthic species in the water column above and below the thermocline in a small eutrophic lake is described. During summer stratification populations of Spirostomum spp, Loxodes spp., Plagiopyla and Deltopylum become established in the plankton on or below the oxycline/thermocline. At shallow sites no migration occurred and populations of the migratory species in the benthos were sparse, with the exception of Plagiopyla which occurred in high densities in the sediment. Two distinct planktonic populations are established during stratification: an epilimnetic community of obligate planktonic ciliates and a hypolimnetic community of benthic migrants.     

Phylogenetic study of benthic, spine-bearing prorocentroids, including Prorocentrum fukuyoi sp. nov.

Species of prorocentroid dinoflagellates are common in marine benthic sediment and epibenthic habitats, as well as in planktonic habitats. Marine planktonic prorocentroids typically possess a small spine in the apical region. In this study, we describe a new, potentially widely distributed benthic species of Prorocentrum, P. fukuyoi sp. nov., from tidal sand habitats in several sites in Australia and from central Japan. This species was found to possess an apical spine or flange and was sister species to P. emarginatum. We analyzed the phylogeny of the group including this new species, based on large subunit (LSU) rDNA sequences. The genus contained a high level of divergence in LSU rDNA, in some cases among sister taxa. P. fukuyoi and P. emarginatum were found to be most closely related to a clade of generally planktonic taxa. Several morphological features may constitute more informative synapomorphies than habitat in distinguishing clades of prorocentroid species.