Unique and fragile diversity emerges from Brazilian caves – two new amphibious species of Xangoniscus Campos-Filho, Araujo & Taiti, 2014 (Oniscidea, Styloniscidae) from Serra do Ramalho karst area, state of Bahia, Brazil

Two new troglobitic species of Xangoniscus are described from two caves of Serra do Ramalho karst area, Bambuí geomorphological group, state of Bahia. Xangoniscus lapaensissp. nov. is described from Gruna Boca da Lapa cave, and X. loboisp. nov. from Gruna da Pingueira II cave. Both species are blind and depigmented and show amphibious habits, as observed for all species of Xangoniscus described until now. Xangoniscus lapaensissp. nov. occurs in travertine pools fed by water of the upper aquifer, and X. loboisp. nov. occurs in a small stream, an upper vadose tributary. Both species occur in fragile microhabitats. Ecological and behavioral data, conservation remarks, and IUCN conservation assessments are included to provide background data for conservation efforts in this unique karst area.

Expended range of Gomphonema firmum (Bacillariophyceae), once considered a Lake Baikal endemic, with notes on the identity of G. lanceolatum var. maximum

This note describes a new record of Gomphonema firmum Skvortzow, which expanded both morphological and distributional ranges of the species. This conspicuous diatom was previously unknown outside of Lake Baikal, where it inhabits deep-water areas. The newly discovered locality belongs to a small stream at a distance of 180 km west from Lake Baikal, where the species was found in a relatively high abundance that enabled to trace a size diminution series including specimens shorter than previously described. In addition, G. lanceolatum var. maximum Poretzky, a name for a diatom from Lake Teletskoe, was included in a synonymy of G. firmum that further expanded the species distribution. In the light of the presented data, the species appears to be a rare diatom with current distribution limited to a few scattered localities in southern Siberia.

Permafrost Dynamics and Degradation in Polar Arctic From Satellite Radar Observations, Yamal Peninsula

We investigate permafrost surface features revealed from satellite radar data in the Siberian arctic at the Yamal peninsula. Surface dynamics analysis based on SRTM and TanDEM-X DEMs shows up to 2 m net loss of surface relief between 2000 and 2014 indicating a highly dynamic landscape. Surface features for the past 14 years reflect an increase in small stream channels and a number of new lakes that developed, likely caused by permafrost thaw. We used Sentinel-1 SAR imagery to measure permafrost surface changes. Owing to limited observation data we analyzed only 2 years. The InSAR time-series has detected surface displacements in three distinct spatial locations during 2017 and 2018. At these three locations, 60–120 mm/yr rates of seasonal surface permafrost changes are observed. Spatial location of seasonal ground displacements aligns well with lithology. One of them is located on marine sediments and is linked to anthropogenic impact on permafrost stability. Two other areas are located within alluvial sediments and are at the top of topographic elevated zones. We discuss the influence of the geologic environment and the potential effect of local upwelling of gas. These combined analyses of InSAR time-series with analysis of geomorphic features from DEMs present an important tool for continuous process monitoring of surface dynamics as part of a global warming risk assessment.

Khao San Dam: The Archaeological Evidence of Burnt Rice Festival in Southern Thailand | ข้าวสารดำา: หลักฐานทางโบราณคดีเกี่ยวกับประเพณีการเผาข้าวในภาคใต้ของ ประเทศไทย

Recently in 2021the 11th office of the Fine Arts Department, Songkhla has reported their annual excavations in Trang Province that archaeologists have found some set of rice while excavation in process namely,1) Khao Kurum Archaeological Site, Huai Yod District and 2) Napala Archaeological Site, Muang District. The artifacts which were found associated with the rice grains on the habitation layer consisted of potsherds, animal bones, grindstone, beads, etc. The grains of rice are short and brown in colour which is examined as carbonized since the beginning at its first left. The primary examination by archaeologists has classified the rice of Napala Archaeological Site as short grain of probably Orysa sativa (Indica or Aus) rice. AMS Radiocarbon dating by Beta Analytic Testing Laboratory shows the AMS standard results and calibration dating of charred material measured radiocarbon age:1440±30BP. Because of their geographical location, both sites are incredibly located on one side of the hill slope, where they were suitable for habitat and plantation, especially tiny paddy fields and farms with sufficient water supply either small stream or well. The found rice, which now still grows uphill, probably called ‘Khao rai’ needs less water or no marsh. Comparative study of ethnographic “Atong” 1 of 12 sub-tribes of the “Garos” Tibeto-Burman in Meghalaya, India which originated slash-and-burnt socio-groups, have shown an interest in growing rice activity. According to their ritual ceremony for planting of paddy, other grain, and seeds takes place. There are many ritualistic offerings of rice such as (1) flattened rice by asking for permission to cultivate the land from the first harvested paddy in May. (2) After the harvesting in September or October, the 1st ceremony of the agricultural year is a thanksgiving ceremony to mark the end of a period of toil in the fields and harvesting of bumper crops, which is probably the most important festival of the Garos locally called “Maidan syla” meant to celebrate the after-harvested festival or burnt rice festival. Their 2nd ceremony is to revive the monsoon clouds. People throw cooked rice on the floor to symbolize hailstones. Noticing the rice, were probably the assemblage of “Khao San Dam” in many activities of these ceremonies, that is the archaeological evidence found in Khao Kurum and Napala Archaeological Sites. In the Southern part of Thailand, once the crops have already cultivated, people celebrate to welcome their outcrops most probably at the end of September to October and mark their end of plantation before the monsoon come. People prepare 4 main rice desserts put together with other necessity stuffs in the “hmrub” special large containers and donate to the ancestors through Buddhist ceremony. Though archaeological evidence shows that southern peninsular was where the migrants from the west especially India origins, who shared same habitat of hillslope, might brought their different traditions through both land trans-peninsular and sea routes then settled down inner western or eastern coast since prehistoric times. The beliefs in animism might belong to some other western migrants and with having “hmrub” is one of their unique cultural characteristic material and tradition remain. Once they settled down then converged to Buddhism, the ritual ceremony may be changed due to religion, but tradition remains the same today, that is, Bun Duean Sib on the 10th of the lunar month or September-October.

Sporidesmiella lignicola sp. nov., a new hyphomycetous fungus from freshwater habitats in China

Freshwater fungi, growing on submerged wood, can promote the degradation of organisms and the reuse of rotten wood energy and play key roles in freshwater ecosystems. Here, a new hyphomycetous fungus, Sporidesmiella lignicola, was isolated and identified from submerged wood samples collected in a small stream in Jiangxi Province, south-eastern China. The new taxon was studied, based on morphological characters and phylogenetic analyses combined with LSU, ITS, TEF1α and RPB2 sequences data. Sporidesmiella lignicola was morphologically characterised by its pink colonies on PDA medium in prophase, macronematous, mononematous, solitary, brown, septate, unbranched, straight or slightly flexuous conidiophores with holoblastic, polyblastic, integrated, terminal, pale brown conidiogenous cells and cylindrical, narrowly clavate, broadly obovoid to cuneiform, 3–4-distoseptate, olivaceous brown or brown conidia with rounded apex. A phylogenetic tree was constructed, based on the combination of LSU, ITS, TEF1α and RPB2 sequences data.

The generation and evolutionary study of novel aptamers for environmental contaminants

<p>The contamination of waterways by environmental pollutants is of growing global concern. The bio-accumulative properties of these contaminants suggest long-term impacts on many species, even those not directly exposed. There is ample evidence of the presence of environmental contaminants within biological fluids of humans, but their effects on health are largely unknown. Understanding the extent of this problem is hampered by labour-intensive extraction techniques that require expensive instrumentation and highly specialised technical expertise. Due to the prohibitive nature of routine analysis, the occurrence of many of these compounds in New Zealand waterways is unknown. Thus, a robust, portable and sensitive biosensor is urgently needed to guide regulatory agencies worldwide. Aptamers are single-stranded nucleic acid molecules that can bind to a specific target molecule with high affinity. Whilst the use of aptamers presents a novel technology to monitor small molecule environmental contaminants, the generation of high affinity aptamers has been limited. The objectives of this PhD study were to: (1) measure key emerging organic contaminants (EOC’s) in a selection of New Zealand waterways covering different land-use types; (2) generate and characterise aptamers that bind three key EOC’s, namely glyphosate, nonylphenol and oxybenzone, and; (3) explore the evolutionary pathways that random nucleotide libraries follow when generating aptamers to a small molecule under different stringencies. A novel bioinformatics pipeline for the analysis of high throughput (HT) SELEX data from multiple selection strategies has been developed and implemented. The conventional method of gas chromatography mass spectrometry (GC-MS) was used to analyse water samples from waterways in the North Island of New Zealand. Technical nonylphenol equivalents and oxybenzone were detected above the minimum detection limit (7.5 ng/L and 0.5 ng/L respectively) at all sampled sites. Concentrations of nonylphenol exceeding environmental guidelines were detected in the Waiwhetu Stream, a small stream within an industrial area in Lower Hutt. The pesticide terbuthylazine was detected at all sampled sites with particular high concentrations in the Waiwhetu and Porirua Stream. Carbendazim (a fungicide) and hexazinone (a herbicide) were also highly prevalent being detected at 87.5% and 75% of sites respectively. Glyphosate was detected at 800 ng/L in both the Waiwhetu Stream and the Porirua Stream. In general, contaminant load was much higher in urban areas than rural or forested areas. These results indicate that EOCs are present in NZ waterways and are likely to be having an impact on aquatic species. The selection of aptamers to three key EOC’s was completed using standard (glyphosate and nonylphenol) and high-throughput (HT) (oxybenzone) SELEX methodologies. DNA aptamers for glyphosate and oxybenzone were successfully generated and characterised. The GLY04 (glyphosate) and OXY-ED7-C1 (oxybenzone) aptamers were characterised using micro-scale thermophoresis and exhibited a Kd of 158 and 107.5 nM, respectively. This is the first report of a glyphosate-binding aptamer in the literature. Attempts to generate a DNA aptamer for nonylphenol were unsuccessful. Whilst five aptamer candidates were generated through 20 rounds of selection, they did not show any evidence of binding to the target molecule. A HT-SELEX approach was utilised to study the effect of different selection parameters on the same starting library during the generation of an oxybenzone aptamer. Six strategies, compared to a standard protocol, were assessed including mutation via error-prone PCR, increased washing volume, increased detergent concentration, higher incubation temperature and negative selection and counter selection. Within each strategy, the frequency and enrichment of candidates at each SELEX round was determined using a novel bioinformatics pipeline. On average, higher frequency candidates were present at the end of SELEX within strategies using higher stringency. Higher enrichment was also observed in the strategy using the most stringent conditions. In summary, this PhD study presents a number of novel findings. The wide-scale presence of key EOC’s in New Zealand waterways was determined. The generation of aptamers that bind to glyphosate and oxybenzone with a nanomolar affinity reveals that aptamers can be generated to such small molecules. This study also resulted in the development of a novel bioinformatics pipeline for HT-SELEX analysis that resulted in a number of recommendations on the design of such experiments. The findings presented herein highlight the possibilities and pitfalls of selecting future aptamers for EOC’s and for implementing HT-SELEX experiments.</p>

The generation and evolutionary study of novel aptamers for environmental contaminants

<p>The contamination of waterways by environmental pollutants is of growing global concern. The bio-accumulative properties of these contaminants suggest long-term impacts on many species, even those not directly exposed. There is ample evidence of the presence of environmental contaminants within biological fluids of humans, but their effects on health are largely unknown. Understanding the extent of this problem is hampered by labour-intensive extraction techniques that require expensive instrumentation and highly specialised technical expertise. Due to the prohibitive nature of routine analysis, the occurrence of many of these compounds in New Zealand waterways is unknown. Thus, a robust, portable and sensitive biosensor is urgently needed to guide regulatory agencies worldwide. Aptamers are single-stranded nucleic acid molecules that can bind to a specific target molecule with high affinity. Whilst the use of aptamers presents a novel technology to monitor small molecule environmental contaminants, the generation of high affinity aptamers has been limited. The objectives of this PhD study were to: (1) measure key emerging organic contaminants (EOC’s) in a selection of New Zealand waterways covering different land-use types; (2) generate and characterise aptamers that bind three key EOC’s, namely glyphosate, nonylphenol and oxybenzone, and; (3) explore the evolutionary pathways that random nucleotide libraries follow when generating aptamers to a small molecule under different stringencies. A novel bioinformatics pipeline for the analysis of high throughput (HT) SELEX data from multiple selection strategies has been developed and implemented. The conventional method of gas chromatography mass spectrometry (GC-MS) was used to analyse water samples from waterways in the North Island of New Zealand. Technical nonylphenol equivalents and oxybenzone were detected above the minimum detection limit (7.5 ng/L and 0.5 ng/L respectively) at all sampled sites. Concentrations of nonylphenol exceeding environmental guidelines were detected in the Waiwhetu Stream, a small stream within an industrial area in Lower Hutt. The pesticide terbuthylazine was detected at all sampled sites with particular high concentrations in the Waiwhetu and Porirua Stream. Carbendazim (a fungicide) and hexazinone (a herbicide) were also highly prevalent being detected at 87.5% and 75% of sites respectively. Glyphosate was detected at 800 ng/L in both the Waiwhetu Stream and the Porirua Stream. In general, contaminant load was much higher in urban areas than rural or forested areas. These results indicate that EOCs are present in NZ waterways and are likely to be having an impact on aquatic species. The selection of aptamers to three key EOC’s was completed using standard (glyphosate and nonylphenol) and high-throughput (HT) (oxybenzone) SELEX methodologies. DNA aptamers for glyphosate and oxybenzone were successfully generated and characterised. The GLY04 (glyphosate) and OXY-ED7-C1 (oxybenzone) aptamers were characterised using micro-scale thermophoresis and exhibited a Kd of 158 and 107.5 nM, respectively. This is the first report of a glyphosate-binding aptamer in the literature. Attempts to generate a DNA aptamer for nonylphenol were unsuccessful. Whilst five aptamer candidates were generated through 20 rounds of selection, they did not show any evidence of binding to the target molecule. A HT-SELEX approach was utilised to study the effect of different selection parameters on the same starting library during the generation of an oxybenzone aptamer. Six strategies, compared to a standard protocol, were assessed including mutation via error-prone PCR, increased washing volume, increased detergent concentration, higher incubation temperature and negative selection and counter selection. Within each strategy, the frequency and enrichment of candidates at each SELEX round was determined using a novel bioinformatics pipeline. On average, higher frequency candidates were present at the end of SELEX within strategies using higher stringency. Higher enrichment was also observed in the strategy using the most stringent conditions. In summary, this PhD study presents a number of novel findings. The wide-scale presence of key EOC’s in New Zealand waterways was determined. The generation of aptamers that bind to glyphosate and oxybenzone with a nanomolar affinity reveals that aptamers can be generated to such small molecules. This study also resulted in the development of a novel bioinformatics pipeline for HT-SELEX analysis that resulted in a number of recommendations on the design of such experiments. The findings presented herein highlight the possibilities and pitfalls of selecting future aptamers for EOC’s and for implementing HT-SELEX experiments.</p>

Morphological description of the final instar larvae of Argia reclusa Selys, 1865 and Tigriagrion aurantinigrum Calvert, 1909 from Southeastern Brazil (Odonata: Coenagrionidae)

The final instar larvae of Argia reclusa Selys, 1865 and Tigriagrion aurantinigrum Calvert, 1909 are described, diagnosed and illustrated. The larvae of A. reclusa has a very prominent premental ligula, shared with a single species in Brazil, from which it can be separated by a combination of characters. The larvae of T. aurantinigrum is similar to most Oxyagrion in regard to prementum and lamellae shape, and differs from those taxa in palpal and premental setation and number of teeth on the labial palp. Both larvae were collected in a small stream of the Cerrado biome, where both species are common.

Pedobacter riviphilus sp. nov., isolated from stream sediment

A Gram-stain-negative, aerobic, motile by gliding, rod-shaped and pink-coloured bacterium, designated strain SW-16T, was isolated from the sediment of small stream in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SW-16T formed a lineage within the genus Pedobacter of the family Sphingobacteriaceae . Phylogenetic analysis also showed that strain SW-16T was most closely related to Pedobacter soli 15-51T (98.0% 16S rRNA gene sequence similarity), Pedobacter humicola R135T (97.5%), Pedobacter suwonensis 15-52T (97.4%), Pedobacter sandarakinus DS-27T (97.0%) and Pedobacter kyungheensis THG-T17T (97.0%). Growth was observed at 10–37 °C (optimum at 30 °C), pH 6–8 (optimum at pH 7) and with 0–2.0 % NaCl (optimum at 0%). The major fatty acids of the bacterial strain were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The predominant respiratory quinone was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified amino lipids, one unidentified phospholipid and three unidentified lipids. The genome size of strain SW-16T was 5.8 Mbp and the G+C content was 38.5 mol%. Based on the results of phenotypic, genomic and phylogenetic analyses, strain SW-16T represents a novel species of the genus Pedobacter , for which the name Pedobacter riviphilus sp. nov. is proposed. The type strain is SW-16T (=KEMB 1602–396T=KCTC 82079T=JCM 34181T).