A biodiversity survey on the planktonic protistan grazers of the Gulf of Naples (Italy)

Plankton communities include both unicellular and multicellular organisms. An important unicellular component is represented by those protists (i.e., unicellular eukaryotes) that are non-strictly autotrophic organisms and consume bacteria and other protists. These organisms are an important link between primary producers and metazoans and are usually known as microzooplankton, protozooplankton, or mixoplankton, as many of them couple phagotrophic and photoautotrophic behaviours. Herein we report on the diversity of these organisms sampled at two sampling sites (coastal and offshore stations), at two depths (0 and 10 m), in the Gulf of Naples during the early autumn of 2020. Despite efforts to list plankton biodiversity of primary producers and metazoan grazers made in this area so far, protistan grazers are still poorly investigated and previous information date back to decades ago. Our survey identified dinoflagellates and oligotrich ciliates as the most abundant groups, while tintinnids were less quantitatively relevant. The taxonomic composition in samples investigated herein remarked that reported by previous studies, with the sole exception of the tintinnid Ascampbeliella armilla, which was never reported before. A coastal-offshore gradient in the taxonomical composition of protistan grazers was also observed, with some species more abundant within coastal waters and other better thriving in offshore ones. Surface and sub-surface communities also differed in terms of species composition, with the deeper communities in the two sites being more similar reciprocally than with communities at the surface. These differences were associated with distinct environmental conditions, such as light availability, as well with the standing feeding environment, arising potential implications in the functioning of the planktonic food web at the local scale.

Rocky reef biodiversity survey: Punta Pardelas, Argentina

Temperate rocky reefs in the SW Atlantic are productive areas that support highly diverse communities of invertebrates, algae and fishes. Rocky outcrops form complex structures which offer a diversity of microhabitats that lead to a great variety of co-existing species. Subtidal biodiversity within the Natural Protected Area Península Valdés is largely unexplored and studies are mainly limited to fish. A total of 560 high definition photoquadrats from seven rocky reefs (1-25 m depth) at Punta Pardelas were obtained during March 2019. In total, 4491 occurrences were recorded and identified to phyla (n = 2), superclasses (n = 1), classes (n = 5), subclasses (n = 2), orders (n = 2), families (n = 1), subfamilies (n = 1), genera (n = 10) and species (n = 43) levels. This dataset was developed to provide a baseline inventory of Punta Pardelas inside the Natural Protected Area, that was only partially reported more than 50 years ago. Such data represent the first step towards monitoring these less-accessible ecosystems. Most of the available information about Atlantic Patagonian marine biodiversity is related to rocky intertidal communities or rocky reef fish communities. Despite having more than 4000 km of coastline, in the last 20 years only four studies have focused on subtidal benthic communities from shallow rocky reefs in Argentina (Genzano et al. 2011, Rechimont et al. 2013, Bravo et al. 2015, Bravo et al. 2020a). However, none of them described the epi-benthic community of different surface orientations on the rocky reefs. This dataset includes several surface orientations (i.e. horizontal, vertical, overhang and cave floor) and their microhabitats. We found almost double the number of taxa previously reported for the area. Through stratified sampling of different surface orientations, we recorded species that are often overlooked and thus registered as part of the existing biodiversity. For example, overhang surfaces in our study showed a unique assemblage and a great diversity of sponges. This work will be valuable as baseline information that is currently out of date in Nuevo Gulf rocky reefs.

Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems

Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.

CONSERVATION, UTILIZATION OF LOCAL PLANT SPECIES, AND CULTIVATION AS THE EFFORTS OF CONTROLLING SALT AND SULFUR LEVELS AT THE BORDER OF BALURAN NATIONAL PARK, SITUBONDO REGENCY, EAST JAVA

The diversity of plant species functions as a shelterbelt, to prevent saltwater intrusion and avoid sulfur from the crater of Mount Ijen through the Banyuputih River in Situbondo Regency. The Situbondo-Banyuwangi area is strategic (Pantura), passing through the Baluran National Park, so it is essential to maintain biodiversity and water ecosystems. Mangroves, beach vegetation, cultivated plants, and forest vegetation are indicators of environmental protection and conservation. This study aims to reveal the diversity of flora species on the border of Baluran National Park, Banyuputih sub-district, Situbondo Regency, which is allegedly contaminated with salt material from the sea and sulfur from the crater of Mount Ijen. An interview was conducted to determine the function of flora, location elevation, water pH, and well depth. The results of the biodiversity survey were then collected and diagnosed, and the scientific name was then determined. Potential species diversity at the border from an altitude of 5 m above sea level (asl) – 62 m asl included 17 families and 29 species. The data on biodiversity, location elevation, water well depth, and pH indicate low sulfur and salt content; therefore, water resources can be used sustainably by the living things surround them.

Fishes from Bassas Da India Atoll in the Mozambique Channel

Bassas da India is a remote, uninhabited coral atoll in the West Indian Ocean. Its inaccessibility had historically precluded study of its ichthyofauna until a small group of scientists from the Oceanographic Research Institute in South Africa undertook a two-week biodiversity survey in 1991. Since then, the discourse on climate change has taken on a higher relevance, calling for protection and study of biodiversity hotspots such as Bassas da India. The survey recorded 309 fish species, including a number of vulnerable teleosts and elasmobranchs. As the only published information on the biodiversity of this remote small island, it is intended that this dataset will contribute to increased relevance as an ecological baseline for detecting impacts relating to climate change in the South West Indian Ocean. Each species is listed in terms of its individual abundance, IUCN status as well as its museum and photographic record. Comparisons are made with survey results of other small coral islands in the region, notably Europa Island, revealing several distinct differences in fish diversity. There is evidence that giant groupers will replace sharks as apex predators when there is no local exploitation. A total of 86 species were photographed to confirm identity, and a further 84 species were provided to the South African Institute for Aquatic Biodiversity museum in Grahamstown and also to several international species experts.

Fishes from Bassas Da India Atoll in the Mozambique Channel

Bassas da India is a remote, uninhabited coral atoll in the West Indian Ocean. Its inaccessibility had historically precluded study of its ichthyofauna until a small group of scientists from the Oceanographic Research Institute in South Africa undertook a two-week biodiversity survey in 1991. Since then, the discourse on climate change has taken on a higher relevance, calling for protection and study of biodiversity hotspots such as Bassas da India. The survey recorded 309 fish species, including a number of vulnerable teleosts and elasmobranchs. As the only published information on the biodiversity of this remote small island, it is intended that this dataset will contribute to increased relevance as an ecological baseline for detecting impacts relating to climate change in the South West Indian Ocean. Each species is listed in terms of its individual abundance, IUCN status as well as its museum and photographic record. Comparisons are made with survey results of other small coral islands in the region, notably Europa Island, revealing several distinct differences in fish diversity. There is evidence that giant groupers will replace sharks as apex predators when there is no local exploitation. A total of 86 species were photographed to confirm identity, and a further 84 species were provided to the South African Institute for Aquatic Biodiversity museum in Grahamstown and also to several international species experts.

On the occurrence of the Himalayan Wolf Canis lupus, L. 1758 (Mammalia: Carnivora: Canidae) in the Gaurishankar Conservation Area, Nepal; its existence confirmed through sign and visual evidence in Rolwaling Valley

The Himalayan Wolf Canis lupus L., a top predator of the Third Pole, is proposed to be of a distinct wolf lineage (C. himalayensis) relative to the Holarctic Grey Wolf as described by mtDNA analyses. A biodiversity survey organized by the Gaurishankar Conservation Area Project (GCAP) has captured images of wolves in three different regions, and the study team has observed wolf scats in five additional regions above the tree line in Rolwaling Valley. Further, interviews with local herders provided evidence of wolf depredation of livestock in the area. The Rolwaling Valley in the Gaurishankar Conservation Area was the study area which was divided into 12, 4 x 4 km (16 km2) grid cells, each supplied with one camera trap operated continuously from June to November 2019 (only 6 out of 12 cameras functioned for the duration of our study). Wolf detections were recorded by camera traps from Yalung Pass (4,956 m), Tsho-Rolpa glacial Lake (4,536 m) and the Dudhkunda ridgeline (5,091 m). The photo capture rate index (PCRI) for wolves was 0.71. Our study reports the first photographic evidence of the Himalayan Wolf in the Rolwaling Valley.

High taxonomic diversity in ship bilges presents challenges for monitoring microbial corrosion and opportunity to utilise community functional profiling

One of the key areas in which microbially influenced corrosion (MIC) has been found to be a problem is in the bilges of maritime vessels. To establish effective biological monitoring protocols, baseline knowledge of the temporal and spatial biological variation within bilges, as well as the effectiveness of different sampling methodologies, is critical. We used 16S rRNA gene metabarcoding of pelagic and sessile bacterial communities from ship bilges to assess the variation in bilge bacterial communities to determine how the inherent bilge diversity could guide or constrain biological monitoring. Bilge communities exhibited high levels of spatial and temporal variation with >80% of the community able to be turned over in the space of 3 months, likely due to disturbance events such as cleaning and maintenance. Sessile and pelagic communities within a given bilge were also inherently distinct, with dominant ESVs rarely shared between the two. Taxa containing KOs associated with dissimilatory sulfate reduction and biofilm production, functions typically associated with MIC, were generally more prevalent in sessile communities. Collectively our findings indicate neither bilge water nor an unaffected bilge from within the same vessel would constitute an appropriate reference community for MIC diagnosis. Optimal sampling locations and strategies that could be incorporated into a standardised method for monitoring bilge biology in relation to MIC were identified. Finally, taxonomic and functional comparisons of bilge diversity highlight the potential of functional approaches in future biological monitoring of MIC and MIC mitigation strategies in general. Importance Microbially influenced corrosion (MIC) has been estimated to contribute 20 - 50% of the costs associated with corrosion globally. Diagnosis and monitoring of MIC is a complex problem requiring knowledge of corrosion rates, corrosion morphology and the associated microbiology to distinguish MIC from abiotic corrosion processes. Historically, biological monitoring of MIC utilised a priori knowledge to monitor sulfate reducing bacteria, however it is becoming widely accepted that a holistic or community-level understanding of corrosion-associated microbiology is needed for MIC diagnosis and monitoring. Before biology associated with MIC attack can be identified, standardised protocols for sampling and monitoring must be developed. The significance of our research is in contributing to the development of robust and repeatable sampling strategies of bilges, which are required for the development of standardised biological monitoring methods for MIC. We achieve this via a biodiversity survey of bilge communities and by comparing taxonomic and functional variation.

Phagotrophic protists (protozoa) in Antarctic terrestrial ecosystems: diversity, distribution, ecology, and best research practices

Phagotrophic protists (formerly protozoa) are a highly diverse, polyphyletic grouping of generally unicellular, heterotrophic eukaryotes that are key regulators of the soil microbiome. The biodiversity and ecology of soil phagotrophic protists are still largely uncharacterized, especially in the Antarctic, which possesses some of the harshest terrestrial environments known and potentially many physiologically unique and scientifically interesting species. Antarctic soil systems are also highly limited in terms of moisture, temperature, and carbon, and the resulting reduced biological complexity can facilitate fine-tuned investigation of the drivers and functioning of microbial communities. To facilitate and encourage future research into protist biodiversity and ecology, especially in context of the broader functioning of Antarctic terrestrial communities, I review the biodiversity, distribution, and ecology of Antarctic soil phagotrophic protists. Biodiversity appears to be highly structured by region and taxonomic group, with the Antarctic Peninsula having the highest taxonomic diversity and ciliates (Ciliophora) being the most diverse taxonomic group. However, richness estimates are likely skewed by disproportionate sampling (over half of the studies are from the peninsula), habitat type bias (predominately moss-associated soils), investigator bias (toward ciliates and the testate amoeba morphogroup), and methodological approach (toward cultivation and morphological identification). To remedy these biases, a standardized methodology using both morphological and molecular identification and increased emphasis on microflagellate and naked amoeba morphogroups is needed. Additionally, future research should transition away from biodiversity survey studies to dedicated ecological studies that emphasize the function, ecophysiology, endemicity, dispersal, and impact of abiotic drivers beyond moisture and temperature.

Optimizing Large-Scale Biodiversity Sampling Effort: Toward an Unbalanced Survey Design

Acquiring marine biodiversity data is difficult, costly, and time-consuming, making it challenging to understand the distribution and abundance of life in the ocean. Historically, approaches to biodiversity sampling over large geographic scales have advocated for equivalent effort across multiple sites to minimize comparative bias. When effort cannot be equalized, techniques such as rarefaction have been applied to minimize biases by reverting diversity estimates to equivalent numbers of samples or individuals. This often results in oversampling and wasted resources or inaccurately characterized communities due to undersampling. How, then, can we better determine an optimal survey design for characterizing species richness and community composition across a range of conditions and capacities without compromising taxonomic resolution and statistical power? Researchers in the Marine Biodiversity Observation Network Pole to Pole of the Americas (MBON Pole to Pole) are surveying rocky shore macroinvertebrates and algal communities spanning ~107° of latitude and 10 biogeographic ecoregions to address this question. Here, we apply existing techniques in the form of fixed-coverage subsampling and a complementary multivariate analysis to determine the optimal effort necessary for characterizing species richness and community composition across the network sampling sites. We show that oversampling for species richness varied between ~20% and 400% at over half of studied areas, while some locations were undersampled by up to 50%. Multivariate error analysis also revealed that most of the localities were oversampled by several-fold for benthic community composition. From this analysis, we advocate for an unbalanced sampling approach to support field programs in the collection of high-quality data, where preliminary information is used to set the minimum required effort to generate robust values of diversity and composition on a site-to-site basis. As part of this recommendation, we provide statistical tools in the open-source R statistical software to aid researchers in implementing optimization strategies and expanding the geographic footprint or sampling frequency of regional biodiversity survey programs.