Epilithic Samples Research Articles

Cymbella liangyanlingii sp. nov. (Bacillariophyta, Cymbellaceae), a new diatom species from the upper tributary of Liujiang River, Guangxi Zhuang Autonomous Region, China

Cymbella liangyanlingii sp. nov. was collected from epilithic samples in the Liujiang River, Guangxi Zhuang Autonomous Region, China. Light microscopy (LM) and scanning electron microscopy (SEM) were used to describe the morphology of the new species, and in addition we provided detailed ecological information about this species. C. liangyanlingii sp. nov. has the features that assign it to the genus Cymbella, including the terminal raphe fissures deflected toward dorsal margin, apical pore fields present at each end on the valve and, for most taxa in the genus, one or more stigmata on the ventral side of the central area. The key diagnostic features that easily distinguish the new species from other similar species: 1) the inconspicuous central area, 2) three slit-like stigmata on the ventral margin, 3) the striae have no interruption on the valve margin, and 4) striae that are mostly uniseriate in the middle and biseriate (5–7) in the ends. This combination of features distinguishes C. liangyanlingii sp. nov. from congers such as C. liyangensis, C. distalebiseriata, C. alexandrovichii and C. hubeiensis. These findings can help us further understand the morphological and ecological information of the genus Cymbella in China.

Sellaphora jiuzhaienis sp. nov. (Bacillariophyceae)—A new diatom species from Jiuzhaigou National Nature Reserve, China

A new species Sellaphora jiuzhaienis sp. nov. was found in epilithic samples from Jiuzhaigou National Nature Reserve, China. The species is described herein as new to science based on light microscopy (LM) and scanning electron microscopy (SEM), and ecological information is provided. The species has linear to linear-elliptic valves, 17.5–33.5 μm long and 7.0–8.5 μm wide and very broad conopeum that occupies almost half of the valve width. The discovery of a new diatom species confirms the importance of Jiuzhaigou not only in terms of species richness and endemicity but also for the biodiversity of freshwater karst ecosystems in the national protected areas of China.

Sellaphora tanghongquii sp. nov. (Bacillariophyta, Sellaphoraceae), a new diatom species from the Southern China

Sellaphora tanghongquii sp. nov. is described from epilithic samples taken from river systems in Southern China. The morphology of the new species is described based on light microscopy (LM) and scanning electron microscopy (SEM), and detailed ecological information is provided. This species has diagnostic features consistent with the genus Sellaphora, including small and linear valves, undulate and filiform raphe, and the presence of internal hymenate occlusions. Compared to morphologically similar species, we found that the new species is the most similar to S. constrictum in valve size and outline, raphe structure, and the external arrangement of the striae. However, S. tanghongquii sp. nov. has the following outstanding features which distinguish from similar species: 1) the valve striae are uniseriate externally and biseriate internally, 2) the shape of areolae are mostly square to elliptical, partly round, oval or irregularly shaped, composed of 2–4 small holes inside externally and round, elliptical, C-shaped, or irregularly shaped internally, 3) undulate valves with a slight constriction near the central portion of the valve, and 4) the presence of a row of separated and small pores on the valve mantle. The species appears to be best assigned to the group of species with axial grooves, which includes the generitype of Sellaphora. The discovery of this new diatom species increases the known biodiversity of the southern regions in China.

Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index.

Recently, several studies demonstrated the usefulness of diatom eDNA metabarcoding as an alternative to assess the ecological quality of rivers and streams. However, the choice of the taxonomic marker as well as the methodology for data analysis differ between these studies, hampering the comparison of their results and effectiveness. The aim of this study was to compare two taxonomic markers commonly used in diatom metabarcoding and three distinct analytical approaches to infer a molecular diatom index. We used the values of classical morphological diatom index as a benchmark for this comparison. We amplified and sequenced both a fragment of the rbcL gene and the V4 region of the 18S rRNA gene for 112 epilithic samples from Swiss and French rivers. We inferred index values using three analytical approaches: by computing it directly from taxonomically assigned sequences, by calibrating de novo the ecovalues of all metabarcodes, and by using a supervised machine learning algorithm to train predictive models. In general, the values of index obtained using the two “taxonomy‐free” approaches, encompassing molecular assignment and machine learning, were closer correlated to the values of the morphological index than the values based on taxonomically assigned sequences. The correlations of the three analytical approaches were higher in the case of rbcL compared to the 18S marker, highlighting the importance of the reference database which is more complete for the rbcL marker. Our study confirms the effectiveness of diatom metabarcoding as an operational tool for rivers ecological quality assessment and shows that the analytical approaches by‐passing the taxonomic assignments are particularly efficient when reference databases are incomplete.

Estructura de la taxocenosis de diatomeas y su relación con variables ambientales en tres cuencas de la provincia de San Luis (Argentina)

La composición y distribución de las asociaciones de algas en ecosistemas lóticos son el resultado de condiciones en el medio ambiente y en particular pueden reflejar su estructura y funcionamiento.El objetivo de este trabajo fue estudiar la relación de la riqueza, abundancia y diversidad de las especies de diatomeas con las características ambientales en tres cuencas de la provincia de San Luis. Para ello se seleccionaron 14 sitios de muestreo en tres cuencas: en la cuenca del río Conlara siete sitios, otros tres en la cuenca del río Quinto y finalmente cuatro en la cuenca del Bebedero. En cada sitio de muestreo se registraron parámetros hidráulicos y fisicoquímicos. Se colectaron muestras epilíticas que fueron obtenidas por raspado de pequeñas rocas del fondo. La estructura de la comunidad estuvo caracterizada por el predominio de las diatomeas pennales que se destacaron tanto cualitativa como cuantitativamente. Las variaciones de parámetros fisicoquímicos influyeron en la composición específica de las taxocenosis y permitieron establecer dos grupos de especies: el primero constituido por Nitzschia palea, Melosira varians, Navicula tripunctata y Halamphora veneta que se vincularon a arroyos de mayor número de orden y mayor conductividad. Mientras que Geissleria decussis, Epithemia sorex y Cymbella affinis constituyeron el segundo grupo relacionado con mayor caudal y pH, en tanto que Navicula radiosa y Rophalodia gibba estuvieron asociadas a la altitud y concentración del oxígeno disuelto, respectivamente. Una referencia florística confiable de diatomeas permite hacer diagnósticos fundamentados sobre el estado ecológico de los arroyos, así como para establecer programas de monitoreo en la provincia.

Contribution to the inventory of Iberian diatoms: <em>Encyonema nevadense</em> S.Blanco & al. sp. nov. (<em>Cymbellales, Gomphonemataceae</em>)

The diatom Encyonema nevadense S.Blanco & al. sp. nov. is described as a new species, from epilithic samples collected from a high mountain pond in Sierra Nevada National Park. This taxon is characterized by the presence of narrow lanceolate valves with a moderate dorsiventrality, and the presence of areolae with irregular external openings. The type population is compared with Encyonema perpusillum (A.Cleve) D.G.Mann and its varieties, the morphologically closest species within the genus. The ecological and biogeographic implications of the discovery are briefly discussed.

Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation.

Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.

Diatom species variation between lake habitats: implications for interpretation of paleolimnological records

A sample of a sediment record contains diatom species that have grown in disparate habitats and eventually accumulated in a deep part of the lake. The original habitats may differ in substrate, depth location, and availability of resources. Identifying the species characteristic of each habitat should improve our ecological and environmental interpretation of the sediment record by distinguishing habitat specific responses. With this aim, we studied the benthic diatom communities of a deep oligotrophic lake across several habitats. The main source of variation in the diatom composition was the substrate type; particularly, sediment biofilms. Depth was the second factor. The thermocline defined a shift in diatom communities that also included changes in the dominant lifeforms. A third factor was the mesoscale heterogeneity (i.e., rock sides). Although most species were present in many habitats, characteristic species were identified for all the main habitats and used for an improved interpretation of the deep sediment record. Appropriate standardization showed increasing species richness and diversity from epilimnetic epilithic samples to hypolimnetic sediment samples. We estimate that more than 5000 valve counts are required for appropriate comparisons. Consequently, in sediment records with lower counts per sample, one has to amalgamate samples—losing temporal resolution—to achieve reliable analyses of diversity changes over time. Deep sediment samples are representative of the gamma-diversity of the lake diatom metacommunity, which result from the local alpha diversity of the habitats and the beta-diversity of the variability in composition among them. This double source of diversity has to be taken into account when using the sediment record for estimating lake biodiversity changes. On the other hand, we show that an estimation of the spatial (habitat) heterogeneity of a reconstructed environmental variable can be achieved using subsets of species characteristic of each habitat. We demonstrate the procedure by reconstructing the pH fluctuations during the last 200 years in several habitats from a single sediment record. The results are coherent with the expected differences between predominantly trophogenic or tropholithic habitats.

Check list of diatom taxa from Vindhyan rivers in Central Highland region

Investigations were undertaken for the first time from the freshwater epilithic diatoms of the Vindhyan Rivers (Ken, Tons, Paisuni), Central Highland, India. Epilithic samples (33 nos) were obtained by scraping an area of 3x3 cm from cobbles at the 11 sampling stations (Ken, Tons, Paisuni) situated between latitude 23o30' to 26o N and longitude 78o30' to 82o30' E. In all 293 diatom taxa (species, varieties and forms) belonging 49 genera were identified, along with some unidentified forms.

Two new needle-shaped Nitzschia taxa from a deep East African crater lake

Two new diatoms, Nitzschia fabiennejansseniana Cocquyt & Ryken sp. nov. and Nitzschia pseudoaequalis Cocquyt sp. nov., are described from Lake Challa, a deep crater lake in East Africa, based on light and electron microscopical observations. These Nitzschia species are morphologically similar to other needle-shaped, planktonic Nitzschia present in freshwater lakes of tropical Africa. The differences between the newly described species and related Nitzschia taxa are a combination of the shape of the poles, the number of striae and fibula in 10 µm, and the presence of a central gap between the fibulae. Nitzschia fabiennejansseniana is common in the plankton of Lake Challa towards the end of the main dry and windy season during the northern hemisphere summer, when deep water-column mixing causes upwelling of nutrient-rich hypolimnetic water. Together with Afrocymbella barkeri, this taxon is the dominant diatom in the pelagic phytoplankton of Lake Challa today, and has been continuously over at least the last several hundreds of years, as recorded in its sediments. The temporal dynamics of both taxa in Lake Challa play a major role in the interpretation of past climate change in equatorial East Africa. The other new taxon, N. pseudoaequalis, was common in some epilithic samples taken from the littoral zone of Lake Challa. It was also sporadically observed in the pelagic phytoplankton near the end of the mixing season.

Response of biofilm growth to experimental warming in a temperate stream

AbstractBiofilm is an important component of small streams, and it is highly sensitive to variations in water temperature. Therefore, it is expectable that the warming predicted for this century will be reflected in its communities. In this study, we investigated the effects of experimental warming on biofilm growth in a small forest stream in Central Portugal. The stream was longitudinally divided in two halves, both at ambient temperature during ambient period; the following months (warmed period), one stream half remained at ambient temperature (control half) and the other half was experimentally warmed by ~3 °C (experimental half), following a before‐after control‐impact design. Biofilm variables (biomass, chlorophyll‐a and chlorophyll‐c concentrations, autotrophic index, and diatom density) were determined from epilithic samples collected from both stream halves three times during the ambient period and five times during the warmed period. The experimental warming led to a significant increase in biomass, chlorophyll‐a, chlorophyll‐c concentration, and diatom density, especially in the winter months. Future warming, especially during the colder months, may thus stimulate biofilm growth, which may strengthen the autotrophic pathways of these systems traditionally based on detritus.

Effects ofDidymosphenia geminatablooms on benthic diatom assemblages in the Restigouche River Watershed, eastern Canada

Nuisance Didymosphenia geminata (Lyngbye) M. Schmidt (didymo) blooms were first reported in 2006 from the Restigouche River Watershed (RRW), eastern Canada. Although government agencies and recreational users are concerned about these blooms, little is known about the impact on biota and (or) the structure and function of the relatively pristine riverine systems of the RRW. Here, we assess whether didymo blooms affect overall benthic diatom assemblage composition by examining epilithic samples from middle stretches of the Patapedia and Upsalquitch rivers. Significant (albeit minor) differences (P < 0.05) in diatom assemblage composition between sites, with and without didymo blooms, were only observed from the Patapedia River. Rarefied diatom species diversity (Hill’s N2) and rarefied richness did not differ significantly among sites, regardless of the presence or absence of blooms. Our data show that didymo blooms have minimal effect on benthic diatom assemblage composition in the RRW.

Comparison of diatom community structure from epilithon and fish guts: implications for inferring past changes in water quality

The sampling skills of three common European fish species (Barbus barbus, Chondrostoma nasus and Squalius cephalus) were tested to assess their potential as biomonitors of past changes in river water quality through the analysis of diatoms in fish guts. The study was performed on three rivers with different chemical and physical conditions. Comparison of similarity indices revealed low diatom assemblage resemblance between epilithic samples and samples collected from fish guts at the same locality. In contrast, a mixed-effect linear model identified significant differences between locations through comparison of diatom-based water quality indices. Among fish species, diatom indices calculated from gut samples of B. barbus and C. nasus were in most cases not significantly different from those from epilithic samples while those from S. cephalus were often significantly different. The results of the study demonstrate that diatom analysis of fish guts provides a clear distinction between eutrophic and hypereutrophic rivers. Finer nutrient variations within hypereutrophic conditions were also found to be significant for some diatom indices. In this context, choice of appropriate diatom water quality index proved to be crucial in maximizing the sensitivity of the method.

Taxonomy, distribution and autecology of Planothidium bagualensis sp. nov. (Bacillariophyta) a common monoraphid species from southern Brazilian rivers

A new species in the genus Planothidium is described, Planothidium bagualensis sp. nov., from rivers of the Rio Pardo hydrographical basin, Rio Grande do Sul, southern Brazil. This account is based on light and scanning electron microscopy. This rather common species was misidentified in previous studies conducted in Brazil as belonging to either a group of species related to Planothidium lanceolatum and its varieties, or Planothidium frequentissimum. The presence of a cavum (“hood”) in the rapheless valve, however, clearly separates it from P. lanceolatum sensu stricto which has only a sinus (“rimmed depression”); the wider and longer cells of P. bagualensis, besides having ultrastructural differences, sets it apart from P. frequentissimum. Planothidium bagualensis is widely reported in freshwater environments of southern Brazil. The species reached up to 45% of relative abundance in epilithic samples from eutrophic lotic environments of the Rio Pardo hydrographical basin. Traditional weighted-averaging approaches (WA) were applied to model phosphates (P), chemical oxygen demand (COD), total dissolved solids and pH optima. P. bagualensis is formally described and the literature reviewed to delimitate its distribution. Published photomicrographs corresponding to Planothidium lanceolatum sensu stricto from South America were up to date only found in the Andean Cordillera (Chile and Bolivia), but until now this taxon has never been illustrated in Brazil.

The response of epilithic diatom assemblages to sewage pollution in mountain streams of the Czech Republic

Background and aim – Mountain streams represent sensitive ecosystems of prime importance for biodiversity conservation. However, the knowledge of the impact of sewage pollution related to intensive recreational exploitation is still limited in these habitats. Our aim was to assess the response of stream diatom assemblages to sewage pollution in the Giant Mountains and the Bohemian Forest, and to find the main factors influencing the community structure. Methods – Epilithic samples from sixteen streams were collected, both in unaffected stream sections and at sites downstream of sewage outflows from mountain cottages or small villages. Basic physical and chemical parameters were measured and relative abundances of diatoms were determined using light microscopy. Key results – A total number of 153 diatom taxa belonging to 44 genera were identified. Based on species data, samples were divided into two groups: the first belonged mainly to sites influenced by pollution, whereas the second consisted of not or slightly affected sites. Both groups were further divided into several subgroups characterised by specific ecological conditions and assemblage composition. Canonical correspondence analysis (CCA) revealed five environmental parameters with significant influence on diatom species composition, some of which were related to sewage pollution (pH, water temperature, discharge volume and concentrations of nitrate nitrogen and organic nitrogen). Conclusions – As a consequence of sewage pollution, oligo- to mesotraphentic taxa were outcompeted by pollution tolerant taxa. However, pollution had no significant influence on diatom diversity, which was similar at sites both upstream and downstream of the outflows. In this study, diatom assemblages performed well as indicators of sewage pollution, and biomonitoring proved to be a useful tool in the detection of environmental stress in mountain streams. Overall, the response of diatom assemblages showed that an increase of recreational activities might significantly alter the ecological status of these ecosystems.

A microbiological study of the self-cleaning potential of oily Arabian Gulf coasts

Due to the active production and transport of crude oil in the Arabian Gulf region, the Arabian Gulf coasts are routinely polluted with oil. Therefore, such coasts have been subject of studies aiming at assessing the roles of indigenous microbial consortia in cleaning these environments. In the present study, epilithic microbial communities along Kuwait coasts were studied for their oil degradation potential. Gravel particles coated with deep green biofilms were collected from four coastal sites in autumn, winter, and spring. Phototrophs in these consortia were determined in terms of their chlorophyll a contents and identified by their morphological characteristics. Total bacteria were counted microscopically and cultivable bacteria by the dilution plating method on nutrient agar as well as on inorganic medium containing oil as a sole source of carbon and energy. The bacterial community structures were also characterized and compared by denaturing gradient gel electrophoresis (DGGE). Epilithic biomass samples from the four sites in the three seasons were rich in diatoms and picocyanobacteria as well as total bacteria. Direct counting gave bacterial numbers per square centimeter gravel surface of 2 to 6 x 10(7) cells depending on the sampling site and season. Cultivable bacterial numbers on nutrient agar and crude oil as a sole source of carbon were 3 x 10(3) to 8 x 10(4) and 1 x 10(3) to 7 x 10(3) cells/cm(2) gravel surface, respectively. The DGGE profiles of epilithon biomass samples revealed major 16S rDNA bands that matched bands of pure oil-utilizing bacterial isolates. The microbial communities showed a degree of consistency in all sites and seasons. The microbial consortia coating gravel particles are potentially suitable tools for self-cleaning of oily Gulf coasts. They are rich in oil-utilizing bacteria whose activities are probably enhanced by oxygen produced by the phototrophic partners in the consortia. The combination of conventional microbiological analysis with molecular approaches gives an enhanced idea about natural microbial communities especially those with environmental application potential.

Epilithic diatoms (Bacillariophyceae) from cloud forest and alpine streams in Bolivia, South America

ABSTRACT A floristic study based on epilithic samples collected from Bolivian cloud forest streams yielded a total of 172 taxa, 41 of which were new or could not be determined based on available literature. Five new taxa at the species and form levels (Gomphonema andinum, G. pumilum var. elegans f. biseriatum, G. pumilum var. rigidum f. biseriatum, Nitzschia boliviana, and N. soratensis) and two new combinations (Pseudostaurosira laucencis and Ulnaria contracta) are presented. Undetermined taxa are only listed herein and a more detailed study will be presented at a later date. The large number of taxa found in only a few samples suggests the Bolivian cloud forests may be a hot spot for epilithic diatom diversity. The use of combined light microscopy (LM) and scanning electron microscopy (SEM) data is of prime importance in the study of this diversity.

Near-Infrared Spectroscopy (NIRS) of Epilithic Material in Streams has a Potential for Monitoring Impact from Mining

There is an increasing demand for cost-effective methods for environmental monitoring, and here we assess the potential of near-infrared spectroscopy (NIRS) on epilithic material from streams (material covering submerged stones) as a new method for monitoring the impact of pollution from mining and mining-related industries. NIRS, a routine technique in industry, registers the chemical properties of organic material on a molecular level and can detect minute alterations in the composition of epilithic material. Epilithic samples from 65 stream sites (42 uncontaminated and 23 contaminated) in northern Sweden were analyzed. The NIRS approach was evaluated by comparing it with the results of chemical analyses and diatom analyses of the same samples. Based on Principal Component Analysis, the NIRS data distinguished contaminated from uncontaminated sites and performed slightly betterthan chemical analyses and clearly betterthan diatom analyses. Of the streams designated a priori as contaminated, 74% were identified as contaminated by NIRS, 65% were identified by chemical analysis, and 26% were identified by diatom analysis. Unlike chemical analyses of water samples, NIRS data reflect biological impacts in the streams, and the epilithic material integrates impact over time. Given that, and the simplicity of NIRS-analyses, further studies to assess the use of NIRS of epilithic material as an inexpensive environmental monitoring method are justified.

Community analysis in stream biomonitoring: what we measure and what we don't

Diatom assemblages from 83 epilithic samples taken from the Mesta River, Bulgaria, were regressed against three sets of predictor variables, i.e. environmental, spatial, and temporal. Redundancy analysis (RDA) of species and environmental data explained 36% of the diatom variance and extracted several important gradients of species distribution, associated with a downstream increase in nutrient levels, pH, temperature, and organic pollution. The inclusion of spatial and temporal variables in the RDA model captured additional 24% of the diatom variance and revealed three more gradients, a spatial gradient represented by higher order polynomial terms of latitude and longitude, and two temporal gradients of annual and seasonal variation. Partial RDAs demonstrated that the unique contribution of each predictor set to the explained diatom variance was the highest in the spatial dataset (16%), followed by the environmental (9%), and the temporal (7%) datasets. The remaining 28% of the variance was explained by the covariance of the predictor sets. This suggests that in biomonitoring of single stream basins, the cheap and simple account of space and time would explain most of the variance in assemblage composition obviating the necessity of expensive and time-consuming environmental assessments. The nature of the underlying environmental mechanisms can be easily inferred from the diatom composition itself.

Algal structure of the littoral epilithon in lentic water bodies at Hope Bay, Antarctic Peninsula

We studied the composition and density of the algae of the littoral epilithon and the taxa turnover in nine lentic water bodies at Hope Bay, Antarctic Peninsula, during summer 2002. At each site we measured the main physical and chemical variables, and took epilithic samples for the algal analysis. Two composed samples (one for qualitative and one for quantitative analysis) were taken randomly about 1 m away from the shore-line of each sampling site. The morphology of the algal mats could be included in the ‘moat and pond type’ in which Cyanobacteria are well represented. A total of 69 algal taxa were recorded in the whole study area. Chlorophyceae showed the highest taxa richness (33%), followed by Cyanobacteria (29%), Bacillariophyceae (26%), Chrysophyceae (10%), and Tribophyceae (2%). As a result of the redundancy analysis performed, we found that the number, composition, and density of taxa in the water bodies at Hope Bay were strongly influenced by nitrate and suspended solids concentrations and by the distance from the sea. The geographical trend in taxa turnover within Hope Bay was explained by elements from the combination of the metapopulation dynamics and the continuum theories, which are related to dispersal limitation and environmental heterogeneity, respectively.