Contrasting dynamics of ciliate communities in sandy and silty sediments of an estuarine intertidal flat

Benthic Heterotrophic Protist Communities of the Southern Baltic Analyzed with the Help of Curated Metabarcoding Studies

Heterotrophic protists are key components of marine ecosystems. They act as controllers of bacterial and microphytobenthos production and contribute significantly to the carbon flux to higher trophic levels. Still, metabarcoding studies on benthic protist communities are much less frequent than for planktonic organisms. Especially in the Baltic Sea, representing the largest brackish water environment on earth, so far, no extensive metabarcoding studies have been conducted to assess the diversity of benthic protists in this unique and diverse habitat. This study aims to give first insights into the diversity of benthic protist communities in two different regions of the Baltic Sea, Fehmarnbelt, and Oderbank. Using amplicon sequencing of the 18S rDNA V9 region of over 100 individual sediment samples, we were able to show significant differences in the community composition between the two regions and to give insights into the vertical distribution of protists within the sediment (0-20 cm). The results indicate that the differences in community composition in the different regions might be explained by several abiotic factors such as salinity and water depth, but are also influenced by methodological aspects such as differences between DNA and RNA results.

Community assembly and co-occurrence network complexity of interstitial microbial communities in the Arctic (investigation of ciliates in the White Sea intertidal zone)

Arctic coastal ecosystems play a major role in global environmental system and have been altered significantly by climate changes. To better understanding the response of marine coastal ecosystems towards rapid Arctic climate changes, we examined the variation in diversity and community structure and provided insights into the co-occurrence network and community assembly of interstitial ciliates in the Kandalaksha Gulf of the White Sea from 2009 to 2019. Co-occurrence networks analysis indicated considerably high ration of positive correlations within a community that indicated low competition between interstitial ciliate species. Furthermore, we found that contribution of stochastic processes to the ciliate community assembly was insignificant. Compare with earlier data from the same ecosystem obtained in 1980s-1990s, the role of competitive factors is decreasing, and communities are becoming more spatially and temporally homogeneous. This community simplification is likely due to the response of the entire intertidal ecosystem to global climate change in Arctic.

The relative roles of multiple drivers on benthic ciliate communities in an intertidal zone

Intertidal biodiversity is being severely disrupted as a result of increased anthropogenic activity. However, our knowledge about how natural gradients, human induced disturbance and biotic interactions affect biodiversity is limited. So, we investigated how three facets of alpha diversity and community composition of benthic ciliates responded to environmental and biological gradients in the intertidal zone of Zhejiang, China. The key determinants and their relative effects on ciliate communities were identified using structural equation modeling, distance-based redundancy analysis and variation partitioning analysis. Our results revealed that sediment grain size was the most important factor affecting alpha diversity and community composition. Human induced eutrophication had significant effects on phylogenetic alpha diversity and community composition. However, the effects of biotic interactions on ciliate communities were relatively small. Moreover, we found community composition was more sensitive to human disturbance than alpha diversity, thus, more suitable for indicating human-induced eutrophication.

Disentangling the relative roles of natural and anthropogenic-induced stressors in shaping benthic ciliate diversity in a heavily disturbed bay

Coastal areas are facing biodiversity loss and degradation of habitats due to intensified human activities. However, our understanding of the relative contribution of natural gradients and human induced disturbance to biodiversity is limited. Here, we investigated the response of three facets of alpha and beta diversity of benthic ciliates to environmental gradients in a highly disturbed estuarine bay in China. We used linear regression and distance-based redundancy analysis to determine the key driving factors for biodiversity. Variation partitioning was further used to examine the relative influence of natural gradients and anthropogenic disturbances on ciliate communities. Our results revealed that ciliate alpha diversity and functional composition remained similar despite notable variation in species composition along salinity gradient. Sediment grain size, together with heavy metals were the strongest determinants in shaping both alpha and beta diversity. After controlling for the effect of natural factors, heavy metals still had significant impacts on beta diversity. Human induced nitrogen enrichment was positively correlated with algivorous functional group with possible impacts on benthic food webs. These results suggest that beta diversity is overall more sensitive to anthropogenic stressors than alpha diversity and give important insights into the role of anthropogenic disturbance on coastal diversity, being also useful for developing ecosystem protection and conservation strategies.

Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing

Eukaryotes are important components of ecosystems in wastewater treatment processes. However, little is known about eukaryotic community in anaerobic wastewater treatment systems. In this study, eukaryotic communities in an up flow anaerobic sludge blanket (UASB) reactor treating domestic sewage during two years of operation were investigated using V4 and V9 regions of 18S rRNA gene for amplicon sequencing. In addition, activated sludge and influent sewage samples were also analyzed and used as the references for aerobic eukaryotic community to characterize anaerobic eukaryotes. The amplicon sequence V4 and V9 libraries detected different taxonomic groups, especially from the UASB samples, suggesting that commonly used V4 and V9 primer pairs could produce a bias for eukaryotic communities analysis. Eukaryotic community structures in the UASB reactor were influenced by the immigration of eukaryotes via influent sewage but were clearly different from the influent sewage and activated sludge. Multivariate statistics indicated that protist genera Cyclidium, Platyophrya and Subulatomonas correlated with chemical oxygen demand and suspended solid concentration, and could be used as bioindicators of treatment performance. Uncultured eukaryotes groups were dominant in the UASB reactor, and their physiological roles need to be examined to understand their contributions to anaerobic processes in future studies.

Environmental status assessment using biological traits analyses and functional diversity indices of benthic ciliate communities

In this study, we tested the hypothesis that the functional diversity of benthic ciliates has high potential to monitor marine ecological status. Therefore, we investigated the spatial and temporal variation of functional diversity of benthic ciliates in the Yangtze Estuary during one year using biological traits analyses and functional diversity indices. Traits and community compositions showed clear spatial and temporal variations. Among a variety of biological traits, feeding type and body size emerged as strongest predictable variables. Functional divergence (FDiv) had an advantage over two other functional diversity indices, as well as over classical diversity measures (i.e. richness, evenness, Shannon-Wiener) to infer environmental status. Significant correlations between biological traits, FDiv and environmental variables (i.e. nutrients, temperature, salinity) suggested that functional diversity of benthic ciliates might be used as a bio-indicator in environmental status assessments. Further mandatory researches need to implement functional diversity of ciliates in routine monitoring programs were discussed.

Benthic ciliate diversity and community composition along water depth gradients: a comparison between the intertidal and offshore areas

The diversity of marine benthic ciliates is largely known from the intertidal zone. No comparative data are available for the change of ciliate communities from the intertidal to offshore sediments in the Yellow Sea. We investigated the community composition and diversity of benthic ciliates at two intertidal (sandy and silty-sand) stations and eight offshore stations along a latitudinal transect in the Yellow Sea. The ciliate abundance and biomass decreased almost linearly with increasing water depth and distance from the intertidal zone. Diversity indices showed a similar trend. By contrast, the total species richness and taxonomic diversity were much higher in the offshore sediments than in the intertidal area. Among the total of 94 species identified, only 20 species were shared by the two habitats, which were characterized by different dominant ciliate assemblages. Carnivorous ciliates always constituted the primary feeding type in terms of biomass at all offshore stations and the intertidal sandy station, whereas at the intertidal silty-sand station the primary feeding group varied throughout the period of sampling. Multivariate analyses indicates the ciliate communities were significantly different between the two habitats. Bottom water temperature and sediment grain size were the key factors that explained the ciliate community structure.

Functional diversity of benthic ciliate communities in response to environmental gradients in a wetland of Yangtze Estuary, China

Researches on the functional diversity of benthic ecosystems have mainly focused on macrofauna, and studies on functional structure of ciliate communities have been based only on trophic- or size-groups. Current research was carried out on the changing patterns of classical and functional diversity of benthic ciliates in response to environmental gradients at three sites in a wetland in Yangtze Estuary. The results showed that changes of environmental factors (e.g. salinity, sediment grain size and hydrodynamic conditions) in the Yangtze Estuary induce variability in species composition and functional trait distribution. Furthermore, increased species richness and diversity did not lead to significant changes in functional diversity due to functional redundancy. However, salt water intrusion of Yangtze Estuary during the dry season could cause reduced functional diversity of ciliate communities. Current study provides the first insight into the functional diversity of ciliate communities in response to environmental gradients.

Ciliate diversity and distribution patterns in the sediments of a seamount and adjacent abyssal plains in the tropical Western Pacific Ocean

Background

Benthic ciliates and the environmental factors shaping their distribution are far from being completely understood. Likewise, deep-sea systems are amongst the least understood ecosystems on Earth. In this study, using high-throughput DNA sequencing, we investigated the diversity and community composition of benthic ciliates in different sediment layers of a seamount and an adjacent abyssal plain in the tropical Western Pacific Ocean with water depths ranging between 813 m and 4566 m. Statistical analyses were used to assess shifts in ciliate communities across vertical sediment gradients and water depth.

Results

Nine out of 12 ciliate classes were detected in the different sediment samples, with Litostomatea accounting for the most diverse group, followed by Plagiopylea and Oligohymenophorea. The novelty of ciliate genetic diversity was extremely high, with a mean similarity of 93.25% to previously described sequences. On a sediment depth gradient, ciliate community structure was more similar within the upper sediment layers (0-1 and 9-10 cm) compared to the lower sediment layers (19-20 and 29-30 cm) at each site. Some unknown ciliate taxa which were absent from the surface sediments were found in deeper sediments layers. On a water depth gradient, the proportion of unique OTUs was between 42.2% and 54.3%, and that of OTUs shared by all sites around 14%. However, alpha diversity of the different ciliate communities was relatively stable in the surface layers along the water depth gradient, and about 78% of the ciliate OTUs retrieved from the surface layer of the shallowest site were shared with the surface layers of sites deeper than 3800 m. Correlation analyses did not reveal any significant effects of measured environmental factors on ciliate community composition and structure.

Conclusions

We revealed an obvious variation in ciliate community along a sediment depth gradient in the seamount and the adjacent abyssal plain and showed that water depth is a less important factor shaping ciliate distribution in deep-sea sediments unlike observed for benthic ciliates in shallow seafloors. Additionally, an extremely high genetic novelty of ciliate diversity was found in these habitats, which points to a hot spot for the discovery of new ciliate species.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1103-6) contains supplementary material, which is available to authorized users.

Distribution of Ciliates in Intertidal Sediments across Geographic Distances: A Molecular View

The estimation of the diversity and geographic distribution of protists in particular ciliates has long been an ongoing debate. We estimated the distribution of ciliates in intertidal sediments with geographic distance ranging from 10cm to 1,000km, using high-throughput DNA sequencing. Higher community similarity, in particular that of rare ciliate taxa, occurred between replicates than between sites. Statistical analyses showed that the community dissimilarities of both abundant and moderately abundant ciliates had correlations with geographic distance at the scales of 50m, 200km and 1000km, indicating a distance-decay relationship. No significant correlation was observed for rare taxa. The analysis of Bray-Curtis similarity showed a higher pairwise community similarity in abundant taxa than in moderately abundant taxa, and that in rare taxa was the lowest. Abundant taxa usually can disperse in a wider range than rare taxa, though their distribution is restricted by distance to some extent. Rare taxa are potentially more sensitive to changing environments, but no distance-decay relationship could be observed. The data indicate contrasting patterns of geographic distribution of the abundant and rare ciliate taxa and a weak distance-decay relationship for relatively abundant taxa at a scale over 50m.

Distributions and biomass of benthic ciliates, foraminifera and amoeboid protists in marine, brackish, and freshwater sediments

The quantitative importance of ciliates, foraminifers, and amoebae was investigated in marine, brackish, and freshwater sediments from 15 littoral stations. Total protozoan communities were usually dominated by ciliates in term of abundance, while amoebae often dominated in terms of biomass. Applying the biomass-metabolic rate equation, ciliates, amoebae, and foraminifera were estimated to contribute 66% of the total abundance and 33% of the biomass, but up to 55% of the combined metabolic rate to the micro- and meiobenthos in the 15 sediments. Statistical analyses using ciliate data demonstrated: (1) species composition and community structures represented significant differences between freshwater and marine/brackish sediments, and subsequently between temperate and arctic sampling sites; (2) the occurrence of dominant ciliates and their allocation to feeding types indicated that herbivory was the most common feeding strategy in these sediments; (3) multivariate analyses showed all of the tested environmental factors (temperature, salinity, silt/clay, carbon, nitrogen, and chlorophyll a) to be important to varying degrees, but especially the combination of salinity, temperature, and silt/clay. Multiple factor effects or comprehensive influences might be important in regulating the distribution of protozoa in sediments. The importance of protozoa in sediment systems and the potential ecological significance of cysts are discussed.

Structure and diversity of intertidal benthic diatom assemblages in contrasting shores: a case study from the Tagus estuary(1)

The structure of intertidal benthic diatoms assemblages in the Tagus estuary was investigated during a 2-year survey, carried out in six stations with different sediment texture. Nonparametric multivariate analyses were used to characterize spatial and temporal patterns of the assemblages and to link them to the measured environmental variables. In addition, diversity and other features related to community physiognomy, such as size-class or life-form distributions, were used to describe the diatom assemblages. A total of 183 diatom taxa were identified during cell counts and their biovolume was determined. Differences between stations (analysis of similarity (ANOSIM), R = 0.932) were more evident than temporal patterns (R = 0.308) and mud content alone was the environmental variable most correlated to the biotic data (BEST, ρ = 0.863). Mudflat stations were typically colonized by low diversity diatom assemblages (H' ~ 1.9), mainly composed of medium-sized motile epipelic species (250-1,000 μm(3) ), that showed species-specific seasonal blooms (e.g., Navicula gregaria Donkin). Sandy stations had more complex and diverse diatom assemblages (H' ~ 3.2). They were mostly composed by a large set of minute epipsammic species (<250 μm(3) ) that, generally, did not show temporal patterns. The structure of intertidal diatom assemblages was largely defined by the interplay between epipelon and epipsammon, and its diversity was explained within the framework of the Intermediate Disturbance Hypothesis. However, the spatial distribution of epipelic and epipsammic life-forms showed that the definition of both functional groups should not be over-simplified.

Effect of bacterial mineralization of phytoplankton-derived phytodetritus on the release of arsenic, cobalt and manganese from muddy sediments in the Southern North Sea. A microcosm study

Muddy sediments of the Belgian Continental Zone (BCZ) are contaminated by metals such as Co, As, Cd, Pb, and Ni. Previous studies have suggested that mineralization of phytodetritus accumulating each year on sediments might cause secondary contaminations of the overlying seawater (metal effluxes). The aim of the present research was to investigate these effluxes using a microcosm approach. Muddy sediments were placed in microcosms (diameter: 15 cm) and overlaid by phytodetritus (a mix of Phaeocystis globosa with the diatom Skeletonema costatum). The final suspension was 130.6 mg L(-1) (dw) and the final chlorophyll a content was 750 ± 35 μg L(-1) (mean ± SD). Natural seawater was used for controls. Microcosms were then incubated in the dark at 15°C during 7 days. Metals were monitored in overlying waters and microbial communities were followed using bacterial and nanoflagellate DAPI counts, thymidine incorporation, community level physiological profiling (CLPP) and fluorescein diacetate analysis (FDA). Benthic effluxes observed in sediments exposed to phytodetritus were always more elevated than those observed in controls. Large effluxes were observed for Mn, Co and As, reaching 1084 nmol m(-2)day(-1) (As), 512 nmol m(-2)day(-1) (Co), and 755 μmol m(-2)day(-1) (Mn). A clear link was established between heterotrophic microbial activity and metal effluxes. The onset of mineralization was very fast and started within 2h of deposition as revealed by CLPP. An increased bacterial production was observed after two days (8.7 mg Cm(-2)day(-2)) and the bacterial biomass appeared controlled by heterotrophic nanoflagellates. Calculations suggest that during phytoplankton blooms the microbial activity alone may release substantial amounts of dissolved arsenic in areas of the BCZ covered by muddy sediments.

Ciliate community structure, diversity and trophic role in offshore sediments from the Yellow Sea

We investigated the community structure, diversity and trophic role of ciliates in the sediments from 48 stations in the Yellow Sea using Ludox density centrifugation and quantitative protargol stain. The ciliate abundance ranged from 1 to 221cellscm(-3) and biomass from 0.0001 to 0.47μgCcm(-3) in the upper 8cm of the sediments. On average, 77% of ciliate abundance and 81% of biomass were distributed in the 0-2cm sediment layers, while the respective proportions were only about 6% and 3% in the 5-8-cm layers. Among the 198 morphospecies, Prostomatea was the most dominant group accounting for 45% of the total abundance and 58% of the total biomass. Carnivorous ciliates constituted the primary feeding type, occupying about 64% of the total biomass, followed by bacterivores (21%), algivores (12%) and omnivores (3%). The ciliate abundance and biomass in the upper 5cm of sediments were two orders of magnitude higher than those in the upper 10m of the Yellow Sea water column. The estimated ciliate bacterivory and herbivory indicate that ciliate ingestion had little direct influence on bacterial standing stock but possibly had an important impact on diatoms in the sediments from the Yellow Sea.

Diversity of oligotrichia and choreotrichia ciliates in coastal marine sediments and in overlying plankton

Elucidating the relationship between ciliate communities in the benthos and the plankton is critical to understanding ciliate diversity in marine systems. Although data for many lineages are sparse, at least some members of the dominant marine ciliate clades Oligotrichia and Choreotrichia can be found in both plankton and benthos, in the latter either as cysts or active forms. In this study, we developed a molecular approach to address the relationship between the diversity of ciliates in the plankton and those of the underlying benthos in the same locations. Samples from plankton and sediments were compared across three sites along the New England coast, and additional subsamples were analyzed to assess reproducibility of methods. We found that sediment and plankton subsamples differed in their robustness to repeated subsampling. Sediment subsamples (i.e., 1-g aliquots from a single approximately 20-g sample) gave variable estimates of diversity, while plankton subsamples produced consistent results. These results indicate the need for additional study to determine the spatial scale over which diversity varies in marine sediments. Clustering of phylogenetic types indicates that benthic assemblages of oligotrichs and choreotrichs appear to be more like those from spatially remote benthic communities than the ciliate communities sampled in the water above them.