Phylogenetic clustering and rarity imply risk of local species extinction in prospective deep-sea mining areas of the Clarion-Clipperton Fracture Zone

An understanding of the forces controlling community structure in the deep sea is essential at a time when its pristineness is threatened by polymetallic nodule mining. Because abiotically defined communities are more sensitive to environmental change, we applied occurrence- and phylogeny-based metrics to determine the importance of biotic versus abiotic structuring processes in nematodes, the most abundant invertebrate taxon of the Clarion-Clipperton Fracture Zone (CCFZ), an area targeted for mining. We investigated the prevalence of rarity and the explanatory power of environmental parameters with respect to phylogenetic diversity (PD). We found evidence for aggregation and phylogenetic clustering in nematode amplicon sequence variants (ASVs) and the dominant genus Acantholaimus, indicating the influence of environmental filtering, sympatric speciation, affinity for overlapping habitats and facilitation for community structure. PD was associated with abiotic variables such as total organic carbon, chloroplastic pigments equivalents and/or mud content, explaining up to 57% of the observed variability and providing further support of the prominence of environmental structuring forces. Rarity was high throughout, ranging from 64 to 75% unique ASVs. Communities defined by environmental filtering with a prevalence of rarity in the CCFZ suggest taxa of these nodule-bearing abyssal plains will be especially vulnerable to the risk of extinction brought about by the efforts to extract them

Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species

Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co-occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next-generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein-encoding genes, with the Complex IV genes (coxI-III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species

Nurturing shared leaders through internship

The Faculty of Social Sciences (the Faculty) of the University of Hong Kong has offered the very first credit-bearing internships in social sciences amongst all local tertiary institutions. Since September 2009, all students in the discipline have to complete 24 credits (equivalent to 4 courses) of off-campus experiential learning, with 12 credits in local internships and another 12 credits in global internships. In June 2012, the Faculty launched the pilot project of Service Leadership Internship (SLI) under the funding of the Li & Fung Service Leadership Initiative, which supports service leadership training in all eight of Hong Kong’s tertiary institution. The SLI took place in the summer 2012 where student interns worked as a team (groups of 3 – 5) to initiate, develop and implement (a) service task(s). By making use of the interns’ multi-disciplinary knowledge, the student interns contributed as shared leaders and helped community partners to generate innovative solutions to authentic problems under different projects. The Faculty also provided a series of support mechanisms to prepare the interns for the SLI projects. For example, an academic tutor was assigned to take care of each SLI project. Also, a series of workshops using the social cognitive approach were organized so as to enhance the interns’ social and personal competence as shared leaders and at the same time understand the construct of leaderships and social responsibilities through experiential learning and discussions. By completing the pre-workshop readings and actively participating in the workshops, interns internalized the core values of leadership such as enhanced self-awareness, became more competent as shared leaders and developed social responsibilities as an active member of the society. Booster sessions were also provided as a platform for small group sharing and problem-solving. In this paper presentation, the overall structure of the SLI, an overview of the content of the internship training and some of the learning outcome of the interns will be shared. The learning experiences in the pilot project will also help us plan for the upcoming summer of SLI 2013. A revised approach on SLI with an expanded participation of community partners will also be shared with the audience

Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments

High‐throughput sequencing has the potential to describe biological communities with high efficiency yet comprehensive assessment of diversity with species‐level resolution remains one of the most challenging aspects of metabarcoding studies. We investigated the utility of curated ribosomal and mitochondrial nematode reference sequence databases for determining phylum‐specific species‐level clustering thresholds. We compiled 438 ribosomal and 290 mitochondrial sequences which identified 99% and 94% as the species delineation clustering threshold, respectively. These thresholds were evaluated in HTS data from mock communities containing 39 nematode species as well as environmental samples from Vietnam. We compared the taxonomic description of the mocks generated by two read‐merging and two clustering algorithms and the cluster‐free Dada2 pipeline. Taxonomic assignment with the RDP classifier was assessed under different training sets. Our results showed that 36/39 mock nematode species were identified across the molecular markers (18S: 32, JB2: 19, JB3: 21) in UClust_ref OTUs at their respective clustering thresholds, outperforming UParse_denovo and the commonly used 97% similarity. Dada2 generated the most realistic number of ASVs (18S: 83, JB2: 75, JB3: 82), collectively identifying 30/39 mock species. The ribosomal marker outperformed the mitochondrial markers in terms of species and genus‐level detections for both OTUs and ASVs. The number of taxonomic assignments of OTUs/ASVs was highest when the smallest reference database containing only nematode sequences was used and when sequences were truncated to the respective amplicon length. Overall, OTUs generated more species‐level detections, which were, however, associated with higher error rates compared to ASVs. Genus‐level assignments using ASVs exhibited higher accuracy and lower error rates compared to species‐level assignments, suggesting that this is the most reliable pipeline for rapid assessment of alpha diversity from environmental samples

Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes

BackgroundThe identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition.MethodologyBoth partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8% vs. 65.8%, respectively) and produced a higher number of bidirectional COI sequences (65.8% vs 39.0%, respectively). A threshold value of 5% K2P genetic divergence marked a clear DNA barcoding gap separating intra- and interspecific distances: 99.3% of all interspecific comparisons were >0.05, while 99.5% of all intraspecific comparisons were <0.05 K2P distance.ConclusionThe I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequence

Active dispersal is differentially affected by inter- and intraspecific competition in closely related nematode species

Competition is one of the main drivers of dispersal, which can be an important mechanism to achieve permanent or temporal coexistence of multiple species. This coexistence can be achieved by a dispersal-competition tradeoff, spatial store effects or neutral dynamics. Here we test the effect of inter- and intraspecific competition on dispersal of four species of the marine nematode species complex Litoditis marina. A previous study in closed microcosms without a possibility for dispersal had demonstrated pronounced interspecific competition, leading to the exclusion of one species. We now investigated whether 1) the dispersal is affected by interspecific interactions, by intraspecific competition (density) or by food availability, 2) the dispersal dynamics influence assemblage composition and can lead to co-occurrence of the species, and 3) the abiotic environment (here salinity) can affect these dynamics. We show that density is the main driver for dispersal in two of the four species. Dispersal of a third species always started at the same time irrespective of density, whereas in the fourth species interspecific interactions accelerated dispersal. Remarkably, this fourth species was not a strong competitor, suggesting that a dispersal–competition tradeoff does not explain the observed coexistence. Salinity did not alter the timing of dispersal when interspecific interactions were present but did affect assemblage composition. Consequently, spatial store effects may influence coexistence. All four species co-occurred in fairly stable abundances throughout the present experiment indicating the importance of species specific dispersal strategies for coexistence. Co-occurrence can be facilitated because competition is postponed or avoided by dispersal. Neutral dynamics also played a role as intra- and interspecific competition were of similar importance in three of the four species. We conclude that dispersal is a driver of the coexistence of closely related nematode species, and that population density and interspecific interactions shape these dynamics

Deep-Sea Nematodes of the Mozambique Channel: Evidence of Random Community Assembly Dynamics in Seep Sediments

Cold seeps occur globally in areas where gases escape from the seafloor, occasionally resulting in the formation of topographic depressions (pockmarks), characterised by unique physicochemical conditions such as anoxic and sulphuric sediments. Free-living marine nematodes tend to dominate the meiofaunal component in such environments, often occurring at extremely high densities and low richness; the mechanisms defining community assembly in areas of fluid seepage, however, have received little attention. Here we focus on a low-activity pockmark at 789 m in the Mozambique Channel (MC). We assessed the diversity, co-occurrence patterns and phylogenetic community structure of nematodes at this bathyal site to that of a nearby reference area as well as abyssal sediments using metabarcoding. In addition, we compared our molecularly-derived diversity estimates to replicate samples identified morphologically. Overall, nematode Amplicon Sequence Variants (ASVs) and generic richness were similar between Pockmark and Abyssal sediments, but lower compared to the Reference area. Although more than half the genera were shared, over 80% of ASVs were unique within each area and even within each replicate core. Even though both methodologies differentiated the Pockmark from the Reference and Abyssal sites, there was little overlap between the molecularly and morphologically identified taxa, highlighting the deficit of reference sequences for deep-sea nematodes in public databases. Phylogenetic community structure at higher taxonomic levels was clustered and did not differ between the three areas yet analysis within three shared and dominant genera (Acantholaimus, Desmoscolex, Halalaimus), revealed randomness with respect to phylogeny as well as co-occurrence which was exclusive to the Pockmark area. These patterns point to the influence of neutral dynamics at this locality resulting from the stochastic sampling of early colonizing taxa, the successional stage at sampling and/or the functional redundancy within the investigated genera