Christer Erséus

The function of marine critical transition zones and the importance of sediment biodiversity

Estuaries and coastal wetlands are critical transition zones (CTZs) that link land, freshwater habitats, and the sea. CTZs provide essential ecological functions, including decomposition, nutrient cycling, and nutrient production, as well as regulation of fluxes of nutrients, water, particles, and organisms to and from land, rivers, and the ocean. Sediment-associated biota are integral to these functions. Functional groups considered essential to CTZ processes include heterotrophic bacteria and fungi, as well as many benthic invertebrates. Key invertebrate functions include shredding, which breaks down and recycles organic matter; suspension feeding, which collects and transports sediments across the sediment–water interface; and bioturbating, which moves sediment into or out of the seabed. In addition, macrophytes regulate many aspects of nutrient, particle, and organism dynamics above- and belowground. Animals moving within or through CTZs are vectors that transport nutrients and organic matter across terrestrial, freshwater, and marine interfaces. Significant threats to biodiversity within CTZs are posed by anthropogenic influences; eutrophication, nonnutrient pollutants, species invasions, overfishing, habitat alteration, and climate change affect species richness or composition in many coastal environments. Because biotic diversity in marine CTZ sediments is inherently low whereas their functional significance is great, shifts in diversity are likely to be particularly important. Species introductions (from invasion) or loss (from overfishing or habitat alteration) provide evidence that single-species changes can have overt, sweeping effects on CTZ structure and function. Certain species may be critically important to the maintenance of ecosystem functions in CTZs even though at present there is limited empirical evidence that the number of species in CTZ sediments is critical. We hypothesized that diversity is indeed important to ecosystem function in marine CTZs because high diversity maintains positive interactions among species (facilitation and mutualism), promoting stability and resistance to invasion or other forms of disturbance. The complexity of interactions among species and feedbacks with ecosystem functions suggests that comparative (mensurative) and manipulative approaches will be required to elucidate the role of diversity in sustaining CTZ functions.

A molecular phylogeny of annelids

We present parsimony analyses of annelids based on the largest taxon sample and most extensive molecular data set yet assembled, with two nuclear ribosomal genes (18S rDNA and the D1 region of 28S rDNA), one nuclear protein coding‐gene (Histone H3) and one mitochondrial ribosomal gene (16S rDNA) from 217 terminal taxa. Of these, 267 sequences are newly sequenced, and the remaining were obtained from GenBank. The included taxa are based on the criteria that the taxon must have 18S rDNA or at least two other loci. Our analyses show that 68% of annelid family ranked taxa represented by more than one taxon in our study are supported by a jackknife value > 50%. In spite of the size of our data set, the phylogenetic signal in the deepest part of the tree remains weak and the majority of the currently recognized major polychaete clades (except Amphinomida and Aphroditiformia) could not be recovered. Terbelliformia is monophyletic (with the exclusion of Pectinariidae, for which only 18S data were available), whereas members of taxa such as Phyllodocida, Cirratuliformia, Sabellida and Scolecida are scattered over the trees. Clitellata is monophyletic, although Dinophilidae should possibly be included, and Clitellata has a sister group within the polychaetes. One major problem is the current lack of knowledge on the closest relatives to annelids and the position of the annelid root. We suggest that the poor resolution in the basal parts of the trees presented here may be due to lack of signal connected to incomplete data sets both in terms of terminal and gene sampling, rapid radiation events and/or uneven evolutionary rates and long‐branch attraction.

Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm

Stable associations of more than one species of symbiont within a single host cell or tissue are assumed to be rare in metazoans because competition for space and resources between symbionts can be detrimental to the host. In animals with multiple endosymbionts, such as mussels from deep-sea hydrothermal vents and reef-building corals, the costs of competition between the symbionts are outweighed by the ecological and physiological flexibility gained by the hosts. A further option for the coexistence of multiple symbionts within a host is if these benefit directly from one another, but such symbioses have not been previously described. Here we show that in the gutless marine oligochaete Olavius algarvensis, endosymbiotic sulphate-reducing bacteria produce sulphide that can serve as an energy source for sulphide-oxidizing symbionts of the host. Thus, these symbionts do not compete for resources but rather share a mutalistic relationship with each other in an endosymbiotic sulphur cycle, in addition to their symbiotic relationship with the oligochaete host.

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late‐Pleistocene age (∼16 000–50 000 years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.

DNA Barcoding Reveals Cryptic Diversity in Lumbricus terrestris L., 1758 (Clitellata): Resurrection of L. herculeus (Savigny, 1826)

The widely studied and invasive earthworm, Lumbricus terrestris L., 1758 has been the subject of nomenclatural debate for many years. However these disputes were not based on suspicions of heterogeneity, but rather on the descriptions and nomenclatural acts associated with the species name. Large numbers of DNA barcode sequences of the cytochrome oxidase I obtained for nominal L. terrestris and six congeneric species reveal that there are two distinct lineages within nominal L. terrestris. One of those lineages contains the Swedish population from which the name-bearing specimen of L. terrestris was obtained. The other contains the population from which the syntype series of Enterion herculeum Savigny, 1826 was collected. In both cases modern and old representatives yielded barcode sequences allowing us to clearly establish that these are two distinct species, as different from one another as any other pair of congeners in our data set. The two are morphologically indistinguishable, except by overlapping size-related characters. We have designated a new neotype for L. terrestris. The newly designated neotype and a syntype of L. herculeus yielded DNA adequate for sequencing part of the cytochrome oxidase I gene (COI). The sequence data make possible the objective determination of the identities of earthworms morphologically identical to L. terrestris and L. herculeus, regardless of body size and segment number. Past work on nominal L. terrestris could have been on either or both species, although L. herculeus has yet to be found outside of Europe.

18S rDNA phylogeny of Clitellata (Annelida)

The phylogeny of Clitellata was analysed using 18S rDNA sequences of a selection of species representing Hirudinida, Acanthobdellida, Branchiobdellida and 10 oligochaetous families. Eleven new 18S sequences of Capilloventridae (one), Haplotaxidae (one), Propappidae (one), Enchytraeidae (two), Lumbricidae (one), Almidae (one), Megascolecidae (two), Lumbriculidae (one), and Phreodrilidae (one) are reported and aligned together with corresponding sequences of 28 previously studied clitellate taxa. Twelve polychaete species were used as an outgroup. The analysis supports an earlier hypothesis based on morphological features that Capilloventridae represents a basal clade of Clitellata; in the 18S tree it shows a sister‐group relationship to all other clitellates. The remaining clitellate taxa form a basal dichotomy, one clade containing Tubificidae (including the former ‘Naididae’), Phreodrilidae, Haplotaxidae, and Propappidae, the other clade with two subgroups: (1) Lumbriculidae together with all leech‐like taxa (Acanthobdellida, Branchiobdellida and Hirudinida), and (2) Enchytraeidae together with a monophyletic group of all earthworms included in the study (Lumbricidae, Almidae and Megascolecidae). These earthworms are members of the taxon Crassiclitellata, the monophyly of which is thus supported by the data. The tree also shows support for the hypothesis that the first clitellates were aquatic. The position of the single species representing Haplotaxidae is not as basal as could have been expected from earlier morphology‐based conclusions about the ancestral status of this family. However, if Haplotaxidae is indeed a paraphyletic assemblage of relict taxa, a higher number of representatives will be needed to resolve its exact relationships with the other clitellates.

Phylogeny of oligochaetous Clitellata

Clitellata, with more than one third of all annelid species described, is briefly introduced, and an overview of the hypotheses of phylogenetic relationships among the groups traditionally referred to as oligochaetes is given. The presentation is placed in a historical context and describes the trend to move from intuitive, narrative approaches to more formal analyses of character patterns. Monophyly of the earthworms (the megadriles, or Metagynophora sensu Jamieson), or at least a major part of them (Crassiclitellata sensu Jamieson), and paraphyly of the ‘microdrile’ largely aquatic, groups are supported by both morphological and molecular data. Further, DNA sequences as well as spermatozoal ultrastructure corroborate that all leech-like taxa (Hirudinida, Acanthobdellida and Branchiobdellida) constitute a clade derived within ‘Oligochaeta’, closely related to the family Lumbriculidae. Molecular systematic studies also support relationships already identified on the basis of morphological data, e.g., the position of Naididae within Tubificidae, the position of Phreodrilidae close to, but outside, the same family, and the putative sister-group relationship between the newly discovered Capilloventridae and the rest of Clitellata. A recent study using 18S rDNA suggests that Enchytraeidae is closely related to Metagynophora, and that these two taxa, which contain all terrestrial oligochaetous clitellates, form a clade derived from aquatic ‘microdriles’ This refutes a recent hypothesis proposing that the ancestor of Clitellata was terrestrial. To a great extent, however, the basal resolution of the oligochaetous clitellates remains unclear.

Coexistence of Bacterial Sulfide Oxidizers, Sulfate Reducers, and Spirochetes in a Gutless Worm (Oligochaeta) from the Peru Margin

ABSTRACT Olavius crassitunicatus is a small symbiont-bearing worm that occurs at high abundance in oxygen-deficient sediments in the East Pacific Ocean. Using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization, we examined the diversity and phylogeny of bacterial symbionts in two geographically distant O. crassitunicatus populations (separated by 385 km) on the Peru margin (water depth, ∼300 m). Five distinct bacterial phylotypes co-occurred in all specimens from both sites: two members of the γ-Proteobacteria (Gamma 1 and 2 symbionts), two members of the δ-Proteobacteria (Delta 1 and 2 symbionts), and one spirochete. A sixth phylotype belonging to the δ-Proteobacteria (Delta 3 symbiont) was found in only one of the two host populations. Three of the O. crassitunicatus bacterial phylotypes are closely related to symbionts of other gutless oligochaete species; the Gamma 1 phylotype is closely related to sulfide-oxidizing symbionts of Olavius algarvensis, Olavius loisae, and Inanidrilus leukodermatus, the Delta 1 phylotype is closely related to sulfate-reducing symbionts of O. algarvensis, and the spirochete is closely related to spirochetal symbionts of O. loisae. In contrast, the Gamma 2 phylotype and the Delta 2 and 3 phylotypes belong to novel lineages that are not related to other bacterial symbionts. Such a phylogenetically diverse yet highly specific and stable association in which multiple bacterial phylotypes coexist within a single host has not been described previously for marine invertebrates.

Cladistic analysis of the subfamilies within the Tubificidae (Oligochaeta)

A hypothesis of phylogenetic relationships within the family Tubificidae is presented, based on a Wagner analysis of morphological characters in the different subfamilies. Two major lincages are recognized. One, including the subfamilies Tubificinae, Telmatodrilinae and Limnodriloidinae, is supported by a synapomorphic ability to form slender spermatozeugmata in the spermathecae; the other, including Rhyacodrilinae (paraphyletic), Phallodrilinae, and the (present family) Naididae, is supported by two synapomorphics, the possession of modified penial setae and numerous coelomocytes (the latter secondarily lost in the Phallodrilinae). Some implications for the classification of the Tubificidae are discussed.

Evaluation of ITS rDNA as a complement to mitochondrial gene sequences for phylogenetic studies in freshwater mussels: an example using Unionidae from north-western Europe

Mitochondrial inheritance in the Unionidae is complex since mitochondria can be inherited from both parents. An increased rate of recombination could lead to erroneous homology assessments, which could cause problems for phylogenetic reconstruction. For this reason we investigated the possibility of using a nuclear marker, the ribosomal internal transcribed spacer region, for phylogenetic studies in the Unionidae, as a complement and comparison to two of the most widely used mitochondrial genes today. The nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S, ITS2) was sequenced from 72 specimens representing six of the seven species of Unionidae mussels occurring in NW Europe: Unio pictorum, U. tumidus, U. crassus, Anodonta anatina, A. cygnea and Pseudanodonta complanata. Sequences from Margaritifera margaritifera were used as an outgroup. The ITS sequences of all species were found to have low intragenomic and infraspecific variation. Compared to mitochondrial genes (16S and COI) they show an intermediate genetic diversity. Phylogenetic analyses produce tree topologies that are congruent with those resulting from analyses of the mitochondrial sequences. Likewise, an incongruence length difference (ILD) test showed no significant incongruence between data sets, indicating that if recombination has occurred it has not produced any conflicting patterns. Best‐resolved and supported trees are obtained when gaps are treated as a fifth character state. A combined analysis of the three gene regions shows that Unio crassus and U. pictorum are more closely related than either to U. tumidus. Pseudanodonta is nested within Anodonta as sister taxon to A. cygnea. Advice on how to best preserve mussel material for DNA studies is provided.