Vertical and horizontal environmental DNA (eDNA) patterns of fish in a shallow and well-mixed North Sea area.

The integration of eDNA metabarcoding into monitoring programs provides valuable information about fish community structures. Despite the growing body of evidence supporting the method's effectiveness in distinguishing fine-scale eDNA signals, there is a limited understanding of eDNA distribution in shallow, well-mixed environments, especially related to sampling depth. We analyzed 167 samples collected from the surface and bottom water at 17 locations of the Belgian Part of the North Sea (BPNS), where the deepest sampling point was 31 m, and compared this to beam trawl catch data collected simultaneously at the same locations. eDNA metabarcoding identified an additional 22 species compared to beam trawl catch data. Diversity measures and patterns were very similar between surface and bottom samples and revealed community patterns that were previously described by long-term beam trawl catch data. Surface and bottom samples had 39 fish species in common, while six and eight rare species were uniquely detected, respectively. Our results demonstrate that eDNA metabarcoding effectively identifies spatial community patterns of fishes in the highly dynamic environment of the BPNS regardless of sampling depth. Out of the six most common species tested, eDNA metabarcoding read abundances correlated strongly with catch-based abundance data for one species, but moderately for two others, indicating that inferring fish abundance and biomass via eDNA metabarcoding remains challenging.

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach.

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

Environmental filtering along a bathymetric gradient: A metabarcoding meta-analysis of free-living nematodes.

Identifying and understanding patterns of biological diversity is crucial at a time when even the most remote and pristine marine ecosystems are threatened by resource exploitation such as deep-seabed mining. Metabarcoding provides the means through which one can perform comprehensive investigations of diversity by examining entire assemblages simultaneously. Nematodes commonly represent the most abundant infaunal metazoan group in marine soft sediments. In this meta-analysis, we compiled all publicly available metabarcoding datasets targeting the 18S rRNA v1-v2 region from sediment samples to conduct a global-scale examination of nematode amplicon sequence variant (ASV) alpha diversity patterns and phylogenetic community structure at different depths and habitats. We found that nematode ASV richness followed a parabolic trend, increasing from the intertidal to the shelf, reaching a maximum in the bathyal and decreasing in the abyssal zone. No depth- or habitat-specific assemblages were identified as a large fraction of genera were shared. Contrastingly, the vast majority of ASVs were unique to each habitat and/or depth zone; genetic diversity was thus highly localized. Overwhelmingly, nematode ASVs in all habitats exhibited phylogenetic clustering, pointing to environmental filtering as the primary force defining community assembly rather than competitive interactions. This finding stresses the importance of habitat preservation for the maintenance of marine nematode diversity.

A fast HRMA tool to authenticate eight salmonid species in commercial food products.

Atlantic and Pacific salmon are frequently consumed species with very different economic values: farmed Atlantic salmon is cheaper than wild-caught Pacific salmons. Species replacements occur with the high valued Pacific species (Oncorhynchus keta, O. gorbuscha, O. kisutch, O. nerka and O. tshawytscha) substituted by cheaper farmed Atlantic salmon (Salmo salar) and Atlantic salmon by rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta). Here we use High-Resolution Melting Analysis (HRMA) to identify eight salmonid species. We designed primers to generate short amplicons of 72 and 116 bp from the fish barcode genes CO1 and CYTB. The time of analysis was under 70 min, after DNA extraction. Food processing of Atlantic salmon (fresh, "Bellevue", "gravadlax", frozen and smoked) did not impact the HRMA profiles allowing reliable identification. A blind test was conducted by three different institutes, showing correct species identifications irrespective of the laboratory conducting the analysis. Finally, a total of 82 retail samples from three European countries were analyzed and a low substitution rate of 1.2% was found. The developed tool provides a quick way to investigate salmon fraud and contributes to safeguard consumers.

Identification and semi-quantification of Atlantic salmon in processed and mixed seafood products using Droplet Digital PCR (ddPCR).

Fishery products are often subject to substitution fraud, which is hard to trace due to a lack of morphologic traits when processed, gutted, or decapitated. Traditional molecular methods (DNA barcoding) fail to identify products containing multiple species and cannot estimate original weight percentages. As a proof of concept, an Atlantic salmon (Salmo salar) specific ddPCR assay was designed to authenticate mixed food products. The method proved to be specific and able to accurately quantify S. salar when using DNA extracts, even in the presence of DNA from closely related salmon species. The ddPCR estimates correlated well with the percentage of S. salar in artificially assembled tissue mixtures. The effect of common salmon processing techniques (freezing, smoking, poaching with a "Bellevue" recipe and marinating with a 'Gravad lax' recipe) on the ddPCR output was investigated and freezing and marinating appeared to lower the copies detected by the ddPCR. Finally, the assay was applied to 46 retail products containing Atlantic or Pacific salmon, and no indications of substitution fraud were detected. The method allows for a semi-quantitative evaluation of the S. salar content in processed food products and can rapidly screen Atlantic salmon products and flag potentially tampered samples for further investigation.

Colonization of macroalgal deposits by estuarine nematodes through air and potential for rafting inside algal structures.

Dispersal is an important life-history trait. In marine meiofauna, and particularly in nematodes, dispersal is generally considered to be mainly passive, i.e. through transport with water currents and bedload transport. Because nematodes have no larval dispersal stage and have a poor swimming ability, their per capita dispersal capacity is expected to be limited. Nevertheless, many marine nematode genera and even species have near-cosmopolitan distributions, and at much smaller spatial scales, can rapidly colonise new habitat patches. Here we demonstrate that certain marine nematodes, like the morphospecies Litoditis marina, can live inside macroalgal structures such as receptacula and-to a lesser extent-floating bladders, which may allow them to raft over large distances with drifting macroalgae. We also demonstrate for the first time that these nematodes can colonize new habitat patches, such as newly deposited macroalgal wrack in the intertidal, not only through seawater but also through air. Our experimental set-up demonstrates that this aerial transport is probably the result of hitchhiking on vectors such as insects, which visit, and move between, the patches of deposited algae. Transport by wind, which has been observed for terrestrial nematodes and freshwater zooplankton, could not be demonstrated. These results can be important for our understanding of both large-scale geographic distribution patterns and of the small-scale colonization dynamics of habitat patches by marine nematodes.

A high-quality genetic reference database for European commercial fishes reveals substitution fraud of processed Atlantic cod (Gadus morhua) and common sole (Solea solea) at different steps in the Belgian supply chain.

Seafood is an important component of the human diet. With depleting fish stocks and increasing prices, seafood is prone to fraudulent substitution. DNA barcoding has illustrated fraudulent substitution of fishes in retail and restaurants. Whether substitution also occurs in other steps of the supply chain remains largely unknown. DNA barcoding relies on public reference databases for species identification, but these can contain incorrect identifications. The creation of a high quality genetic reference database for 42 European commercially important fishes was initiated containing 145 Cytochrome c oxidase subunit I (COI) and 152 Cytochrome b (cytB) sequences. This database was used to identify substitution rates of Atlantic cod (Gadus morhua) and common sole (Solea solea) along the fish supply chain in Belgium using DNA barcoding. Three out of 132 cod samples were substituted, in catering (6%), import (5%) and fishmongers (3%). Seven out of the 41 processed sole samples were substituted, in wholesale (100%), food services (50%), retailers (20%) and catering (8%). Results show that substitution of G. morhua and S. solea is not restricted to restaurants, but occurs in other parts of the supply chain, warranting for more stringent controls along the supply chain to increase transparency and trust among consumers.

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.

Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea.

Nonindigenous species pose a major threat for coastal and estuarine ecosystems. Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotyping-by-sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F ST .02-.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F ST .36-.39; p < .01). This study demonstrates the utility of GBS to investigate fine-scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at: The DNA sequences generated for this study are deposited in the NCBI sequence read archive under SRA accession numbers SRR6950721-SRR6950884, and will be made publically available upon publication of this manuscript.

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.

Living apart-together: Microhabitat differentiation of cryptic nematode species in a saltmarsh habitat.

Coexistence of highly similar species is at odds with ecological theory of competition; coexistence, then, requires stabilizing mechanisms such as differences in ecological niche. In the bacterivore nematode Litoditis marina species complex, which occurs associated with macro-algae, four cryptic lineages (Pm I-IV) co-occur in the field along the south-western coast and estuaries of The Netherlands. Here we investigate the temporal and/or spatial niche differentiation in their natural environment using a qPCR-based detection and relative quantification method. We collected different algal species (i.e. two Fucus species and Ulva sp.) and separated algal structures (i.e. receptacula, thalli, non-fertile tips and bladders) at different sampling months and times (i.e. twice per sampling month), to examine differences in microhabitat use between coexisting L. marina species. Results demonstrate that the cryptic species composition varied among different algal species and algal structures, which was also subject to temporal shifts. Pm I dominated on Fucus spp., Pm II showed dominance on Ulva sp., while Pm III overall had the lowest frequencies. Microhabitat partitioning was most pronounced between the two cryptic species which had similar microbiomes (Pm I and Pm II), and less so between the two species which had significantly different microbiomes (Pm I and Pm III), suggesting that species which share the same microhabitats may avoid competition through resource partitioning. The interplay of microhabitat differentiation and temporal dynamics among the cryptic species of L. marina implies that there is a complex interaction between biotic components and abiotic factors which contributes to their coexistence in the field.

Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids.

The detection of external and internal cues alters gene expression in the brain which in turn may affect neural networks that underly behavioral responses. Previous studies have shown that gene expression profiles differ between major brain regions within individuals and between species with different morphologies, cognitive abilities and/or behaviors. A detailed description of gene expression in all macroanatomical brain regions and in species with similar morphologies and behaviors is however lacking. Here, we dissected the brain of two cichlid species into six macroanatomical regions. Ophthalmotilapia nasuta and O. ventralis have similar morphology and behavior and occasionally hybridize in the wild. We use 3' mRNA sequencing and a stage-wise statistical testing procedure to identify differential gene expression between females that were kept in a social setting with other females. Our results show that gene expression differs substantially between all six brain parts within species: out of 11,577 assessed genes, 8,748 are differentially expressed (DE) in at least one brain part compared to the average expression of the other brain parts. At most 16% of these DE genes have |log2FC| significantly higher than two. Functional differences between brain parts were consistent between species. The majority (61-79%) of genes that are DE in a particular brain part were shared between both species. Only 32 genes show significant differences in fold change across brain parts between species. These genes are mainly linked to transport, transmembrane transport, transcription (and its regulation) and signal transduction. Moreover, statistical equivalence testing reveals that within each comparison, on average 89% of the genes show an equivalent fold change between both species. The pronounced differences in gene expression between brain parts and the conserved patterns between closely related species with similar morphologies and behavior suggest that unraveling the interactions between genes and behavior will benefit from neurogenomic profiling of distinct brain regions.

The effect of bio-irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene.

The presence of large densities of the piston-pumping polychaete Lanice conchilega can have important consequences for the functioning of marine sediments. It is considered both an allogenic and an autogenic ecosystem engineer, affecting spatial and temporal biogeochemical gradients (oxygen concentrations, oxygen penetration depth and nutrient concentrations) and physical properties (grain size) of marine sediments, which could affect functional properties of sediment-inhabiting microbial communities. Here we investigated whether density-dependent effects of L. conchilega affected horizontal (m-scale) and vertical (cm-scale) patterns in the distribution, diversity and composition of the typical nosZ gene in the active denitrifying organisms. This gene plays a major role in N2O reduction in coastal ecosystems as the last step completing the denitrification pathway. We showed that both vertical and horizontal composition and richness of nosZ gene were indeed significantly affected when large densities of the bio-irrigator were present. This could be directly related to allogenic ecosystem engineering effects on the environment, reflected in increased oxygen penetration depth and oxygen concentrations in the upper cm of the sediment in high densities of L. conchilega. A higher diversity (Shannon diversity and inverse Simpson) of nosZ observed in patches with high L. conchilega densities (3,185-3,440 ind. m-2) at deeper sediment layers could suggest a downward transport of NO3- to deeper layers resulting from bio-irrigation as well. Hence, our results show the effect of L. conchilega bio-irrigation activity on denitrifying organisms in L. conchilega reefs.

Limited possibilities for prezygotic barriers in the reproductive behaviour of sympatric Ophthalmotilapia species (Teleostei, Cichlidae).

Since prezygotic rather than postzygotic barriers are believed to maintain the diversity of closely related sympatric cichlids, differences in phenotypic traits and reproductive behaviours are likely involved in maintaining species boundaries. Here, we focused on the reproductive behaviour of three Ophthalmotilapia species with distributions that only overlap on a small stretch of the shore line of Lake Tanganyika. Repeated introgression of mitochondrial DNA between these species was previously reported, which suggested they can hybridise. Our aim is to test the hypothesis that reproductive behaviour acts as a prezygotic barrier that prevents frequent hybridisation in sympatric Ophthalmotilapia species. We performed a quantitative analysis of twelve reproductions (four for O. ventralis, six for O. nasuta, one for O. boops, and one between a female O. ventralis and a male O. nasuta). Although similar ethograms were obtained for these reproductions, the O. ventralis and O. boops males displayed a behaviour that was never performed by O. nasuta males. This behaviour was displayed during courtship and we called it 'invite'. In O. ventralis, we could show that it was associated with the emission of a single pulse sound. The comparison of O. nasuta and O. ventralis reproductive behaviours also revealed some quantitative differences: O. ventralis males showed the location of the bower more often to the female, whereas O. ventralis females followed the male more often. The similarity between the reproductive behaviours in O. ventralis and O. nasuta could explain the occurrence of the heterospecific spawning event recorded between an O. nasuta male and an O. ventralis female. Importantly, few eggs were laid and the maternal mouthbrooding that resulted from this heterospecific reproduction only lasted for two days, which suggested the abortion of egg development. Hence, in the absence of conspecifics, courtship and mating behaviours alone do not constitute perfect prezygotic barriers between these two species.

Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

BACKGROUND: There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. RESULTS: Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. CONCLUSIONS: The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments.

BACKGROUND: Dispersal ability, population genetic structure and species divergence in marine nematodes are still poorly understood, especially in remote areas such as the Southern Ocean. We investigated genetic differentiation of species and populations of the free-living endobenthic nematode genera Sabatieria and Desmodora using nuclear 18S rDNA, internal transcribed spacer (ITS) rDNA, and mitochondrial cytochrome oxidase I (COI) gene sequences. Specimens were collected at continental shelf depths (200-500 m) near the Antarctic Peninsula, Scotia Arc and eastern side of the Weddell Sea. The two nematode genera co-occurred at all sampled locations, but with different vertical distribution in the sediment. A combination of phylogenetic (GMYC, Bayesian Inference, Maximum Likelihood) and population genetic (AMOVA) analyses were used for species delimitation and assessment of gene flow between sampling locations. RESULTS: Sequence analyses resulted in the delimitation of four divergent species lineages in Sabatieria, two of which could not be discriminated morphologically and most likely constitute cryptic species. Two species were recognised in Desmodora, one of which showed large intraspecific morphological variation. Both genera comprised species that were restricted to one side of the Weddell Sea and species that were widely spread across it. Population genetic structuring was highly significant and more pronounced in the deeper sediment-dwelling Sabatieria species, which are generally less prone to resuspension and passive dispersal in the water column than surface Desmodora species. CONCLUSIONS: Our results indicate that gene flow is restricted at large geographic distance in the Southern Ocean, which casts doubt on the efficiency of the Weddell gyre and Antarctic Circumpolar Current in facilitating circum-Antarctic nematode species distributions. We also show that genetic structuring and cryptic speciation can be very different in nematode species isolated from the same geographic area, but with different habitat preferences (surface versus deeper sediment layers).

Low genetic but high morphological variation over more than 1000 km coastline refutes omnipresence of cryptic diversity in marine nematodes.

BACKGROUND: The resilience of ecosystems to negative impacts is generally higher when high gene flow, species diversity and genetic diversity are present. Population genetic studies are suitable to investigate genetic diversity and estimate gene flow between populations. Seaweed beds form a dynamic shallow water ecosystem influenced by climate change and human exploitation, as such, seaweed beds are a particularly powerful model to investigate ecosystem resilience in coastal areas. We studied the population genetic structure of the new nematode species Paracanthonchus gynodiporata associated with seaweeds in northeastern Brazil. Nematodes are generally believed to have a limited dispersal capacity because of the lack of planktonic larvae. Yet, they can drift on seaweeds, and water currents might be a natural barrier for their dispersal. Populations of P. gynodiporata were sampled over more than 1000 km coastline in regions across major oceanic currents with and without historical exploitation of seaweed. RESULTS: P. gynodiporata is described in an integrative way using mitochondrial and nuclear sequences and morphological data. The 3D model of the head region shows for the first time a detailed view of the ventrosublateral teeth, a character often overlooked in older taxonomic studies of the genus. A total of 17 mitochondrial COI haplotypes were found with one haplotype representing 63 to 83% of the frequencies in each population. AMOVA showed overall little population genetic structure (F ST = 0.05204), and no genetic subdivision between the populations under the influence of the two different water currents were found. Effects of historical seaweed exploitation on population genetic diversity were not detected. In contrast, significant differences between populations were found in morphometric characters. This discrepancy in genetic and morphological differentiation between populations across 1000 km of coastline is surprising in view of the frequently observed presence of several cryptic species at small geographical scale in other macroalgal associated nematodes. CONCLUSIONS: Our results show that cryptic species are not omnipresent in marine nematode species, suggesting that nematodes associated with seaweeds have been able to disperse over large distances across well-known biogeographic barriers.

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.

Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats.

Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The Håkon Mosby mud volcano (Barents Sea, 1,280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulfide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 individuals 10 cm(-2)). Halomonhystera hermesi is a member of the intertidal Halomonhystera disjuncta species complex that includes five cryptic species (GD1-5). GD1-5's common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi's closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulfide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signaling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signaling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was approximately 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC-rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible preadaptation to low oxygen and high sulfide levels might have played an important role in the establishment of a cold-seep Halomonhystera population.

Daily Temperature Fluctuations Alter Interactions between Closely Related Species of Marine Nematodes.

In addition to an increase in mean temperature, climate change models predict decreasing amplitudes of daily temperature fluctuations. In temperate regions, where daily and seasonal fluctuations are prominent, such decreases in daily temperature fluctuations can have a pronounced effect on the fitness of species and on the outcome of species interactions. In this study, the effect of a temperature regime with daily fluctuations versus a constant temperature on the fitness and interspecific interactions of three cryptic species of the marine nematode species complex of Litoditis marina (Pm I, Pm III and Pm IV) were investigated. In a lab experiment, different combinations of species (monospecific treatment: Pm I and Pm IV and Pm III alone; two-species treatment: Pm I + Pm IV; three-species treatment: Pm I + Pm IV + Pm III) were subjected to two different temperature regimes: one constant and one fluctuating temperature. Our results showed that fluctuating temperature had minor or no effects on the population fitness of the three species in monocultures. In contrast, interspecific interactions clearly influenced the fitness of all three species, both positively and negatively. Temperature regime did have a substantial effect on the interactions between the species. In the two-species treatment, temperature regime altered the interaction from a sort of mutualism to commensalism. In addition, the strength of the interspecific interactions changed depending on the temperature regime in the three-species treatment. This experiment confirms that interactions between the species can change depending on the abiotic environment; these results show that it is important to incorporate the effect of fluctuations on interspecific interactions to predict the effect of climate change on biodiversity.