Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds.

Unsupervised Machine Learning and Data Mining Procedures Reveal Short Term, Climate Driven Patterns Linking Physico-Chemical Features and Zooplankton Diversity in Small Ponds

Machine Learning (ML) is an increasingly accessible discipline in computer science that develops dynamic algorithms capable of data-driven decisions and whose use in ecology is growing. Fuzzy sets are suitable descriptors of ecological communities as compared to other standard algorithms and allow the description of decisions that include elements of uncertainty and vagueness. However, fuzzy sets are scarcely applied in ecology. In this work, an unsupervised machine learning algorithm, fuzzy c-means and association rules mining were applied to assess the factors influencing the assemblage composition and distribution patterns of 12 zooplankton taxa in 24 shallow ponds in northern Italy. The fuzzy c-means algorithm was implemented to classify the ponds in terms of taxa they support, and to identify the influence of chemical and physical environmental features on the assemblage patterns. Data retrieved during 2014 and 2015 were compared, taking into account that 2014 late spring and summer air temperatures were much lower than historical records, whereas 2015 mean monthly air temperatures were much warmer than historical averages. In both years, fuzzy c-means show a strong clustering of ponds in two groups, contrasting sites characterized by different physico-chemical and biological features. Climatic anomalies, affecting the temperature regime, together with the main water supply to shallow ponds (e.g., surface runoff vs. groundwater) represent disturbance factors producing large interannual differences in the chemistry, biology and short-term dynamic of small aquatic ecosystems. Unsupervised machine learning algorithms and fuzzy sets may help in catching such apparently erratic differences.

An account of epiphytic diatoms in mediterranean wetlands: comparing morphological and molecular assessments

Benthic diatoms are well known bioindicators of water quality, used in many aquatic ecosystems. Since diatom-based monitoring of water quality is required by European legislation, the search for methods that facilitate this task has become more relevant. The aim of this study was to test the reliability of DNA metabarcoding combined with high-throughput sequencing (HTS) techniques in the bioassessment of 22 Mediterranean shallow ponds in Spain. For each pond, Trophic Diatom Index (TDI) was calculated from inventories obtained by using light microscopy, and then molecular (HTS) methods. Ponds were subsequently classified into five water quality classes. Our results showed a good correspondence between both methods, especially after applying a correction factor depending on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, mainly those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Therefore, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to traditional ones in Mediterranean shallow ponds.

Chaoborus flavicans Meigen (Diptera, Chaoboridae) is a complex of lake and pond dwelling species: a revision

Chaoborus flavicans (Meigen) is a widespread and much studied lacustrine phantom midge. As larvae, these insects are important aquatic predators. Based on the available type material, morphology of immature stages and adults, their aquatic habitat, and DNA barcodes, C. flavicans is shown to be a composite of at least four species, with three of these named here. Chaoborus flavicans is primarily a lake-dwelling species with a Holarctic range. Chaoborus albipes (Johannsen, 1903 stat. rev.) and C. posio Salmela sp. n. are pond-dwelling Holarctic and north European species, respectively. The position of the larval subordinate mandibular tooth at the vertex of the second and fourth teeth is a synapomorphy of the Chaoborus flavicans species complex. We present an identification key to fourth instar larvae, pupae, and adult males. We also designate the lectotype and paralectotypes of Sayomyia rotundifolia Felt, 1904 (syn. nov. of C. albipes). We hypothesize that a fourth species of the species complex is present in Japan. Our revision indicates that Holarctic shallow ponds contain a hidden diversity of predators (C. albipes and C. posio sp. n.).

Haematological and biochemical blood profile of African catfish (Clarias gariepinus) cultured in ponds of different water depth and fed sinking versus floating diet

This study contributes data on haematological and biochemical parameters of African catfish, Clarias gariepinus. It employed a 3 ? 2 factorial design with three ponds of different water depth (0.5, 1 and 1.5 m) and two types of feed (floating and sinking). Twelve earthen ponds (1 m x 2 m) were stocked with 16 fingerlings catfish each (mean weight ~100g) and their blood parameters were monitored over 12 weeks. Differences in hematological parameters related to water depth were mostly significant, and better results were recorded in fish reared in shallower water ponds. Feed type showed improved hematological parameters with using of sinking diet. Most biochemical parameters showed significant differences in pond waters depth and feed type with better results coincided with rearing fish in shallower water depth and with sinking feed. Conclusively, culturing Catfish in shallow ponds (0.5 m) and use of sinking feed improve physiological response and health condition.

Distribution and status of Howell’s Quillwort (Isoetes howellii, Isoetaceae) in Canada and its relation to Bolander’s Quillwort (Isoetes bolanderi)

The sparsely documented lycophyte, Howell’s Quillwort (Isoetes howellii), occurs in Canada in four distinct areas of British Columbia in a variety of microhabitats. Before 2010, two areas of occurrence were known in Canada. Two additional clusters of occurrences have been discovered in the last decade. In Canada, I. howellii is found in open, ephemeral wet swales, shallow ponds, and periodically flooded shorelines, channels, and back beach meadows. Habitat rarity may be the primary reason for the large gaps between areas of occurrence. The current viability of the Canadian population is dependent on maintaining the recently discovered large number of individuals in the North Thompson River Region. Isoetes howellii shares many similarities with fellow diploid, Bolander’s Quillwort (Isoetes bolanderi). The possibility that it represents a low-elevation subspecies of I. bolanderi requires further investigation. Isoetes howellii is rare in British Columbia and warrants consideration as a species at risk in Canada.

Ecosystem Metabolism in Small Ponds: The Effects of Floating-Leaved Macrophytes

Small ponds constitute a significant number of standing water bodies on earth and may contribute to CO2 uptake or release into the atmosphere. Despite their importance, few studies have examined ecosystem metabolism in ponds, especially in ponds that may be dominated by floating-leaved macrophytes. In this study, we examined ecosystem metabolism by measuring changes in dissolved oxygen levels every 10 min from late May through late October for four shallow ponds (0.5–1.5 m) in east-central Minnesota, USA. Ponds had varying levels of floating-leaved macrophytes from sparse (<1% coverage) to abundant (61% coverage). We found significant differences in a number of physical/chemical factors including P, N, DOC, water temperature and light penetration. We also found significant difference in gross primary production (GPP—average ranged from 2.2 to 5.5 mg O2/L/day), respiration (R—average ranged from −6.8 to −3.6 mg O2/L/day) and net ecosystem production (NEP—average ranged from −1.5 to −0.1 mg O2/L/day) among the ponds. On average, all of the ponds were heterotrophic (R > GPP). While it appeared that floating-leaved macrophytes provided a significant impact on ecosystem metabolism, there was not a one-to-one correspondence between the amount of macrophytes and the level of ecosystem metabolism.

Pengaruh Liang Boleophthalmus pectinirostris (Linnaeus, 1758) (Actinopterygii:Gobiidae) terhadap Biomassa Mikrofitobenthos di Ekosistem Mangrove Pandansari Brebes Jawa Tengah

Mudskippers (Boleophthalmus pectinirostris) in temperate climates make burrows and shallow ponds surrounded by mud walls as a provider of microhabitats for microphytobenthos. In the mangrove ecosystem of Pandansari Brebes there are also Boleophthalmus pectinirostris which make burrows. The purpose of this study is to determine the effect of the Boleophthalmus pectinirostris burrow as a microhabitat for microphytobenthos in the mangrove ecosystem of Pandansari, Kaliwlingi village, Brebes. This research was conducted in mangrove and mudflat beach areas with three transects and three replications each. Samples were taken were burrow structures, temperature, and microphytobenthos biomass in the inner and outer area of the burrow. The results showed a total area of burrows in mudflat beach areas 71.93 ± 24.9cm2/m2 was greater than in mangrove areas 50.51 ± 46.9cm2/m2 because the beach has more mud than in mangrove. Microphytobenthos biomass was fewer in mudflat beach areas than mangrove areas because the density of Boleophthalmus pectinirostris was more on the mudflat. There was no difference in microphytobenthos biomass inside the burrow (mangrove: 1623 ± 1108µg/mm2; mudflat beach: 94.5 ± 67.5µg/mm2) from outside the burrow (mangrove: 2484 ± 3161µg/mm2; mudflat beach: 145 ± 151µg/mm2). This shows that the Boleophthalmus pectinirostris burrow in Pandansari Brebes does not provide microhabitats for microphytobenthos. This is because in the tropics the temperature is almost the same every year so that microphytobenthos can always live every year. Ikan gelodok (Boleophthalmus pectinirostris) di daerah beriklim temperate membuat liang dan juga kolam dangkal yang di kelilingi oleh dinding lumpur sebagai penyedia mikrohabitat bagi mikrofitobenthos. Di ekosistem mangrove Pandansari Brebes juga terdapat B. pectinirostris yang membuat liang. Tujuan penelitian ini mengetahui pengaruh liang ikan gelodok jenis B. pectinirostris sebagai mikrohabitat bagi mikrofitobenthos di ekosistem mangrove daerah Pandansari desa Kaliwlingi Brebes. Penelitian ini dilakukan di daerah mangrove dan daerah pantai berlumpur dengan masing tiga transek dan tiga ulangan. Sampel yang diambil berupa struktur liang, suhu dan biomassa mikrofitobenthos di area dalam dan luar liang. Hasil menunjukan luas liang total lebih besar di daerah pantai 71,93±24,9 cm2/m2 karena pantai memiliki lumpur yang banyak daripada di daerah mangrove 50,51±46,9cm2/m2. Biomassa mikrofitobenthos lebih sedikit di daerah pantai daripada daerah mangrove karena kepadatan B. pectinirostris lebih banyak di pantai. Tidak ada perbedaan biomassa mikrofitobenthos secara signifikan di dalam liang (mangrove: 1623±1108µg/mm2; pantai: 94,5±67,5µg/mm2) dengan di luar liang (mangrove: 2484±3161µg/mm2; pantai:145±151µg/mm2) hal ini menunjukan liang B. pectinirostris di Pandansari Brebes tidak menyediakan mikrohabitat bagi mikrofitobenthos. Hal ini disebabkan di daerah tropis suhu tiap tahun yang hampir sama sehingga mikrofitobenthos dapat selalu hidup tiap tahun