‘Candidatus Aquirickettsiella gammari’ (Gammaproteobacteria: Legionellales: Coxiellaceae): A bacterial pathogen of the freshwater crustacean Gammarus fossarum (Malacostraca: Amphipoda)

Disentangling the determinants of symbiotic species richness in native and invasive gammarids (Crustacea, Amphipoda) of the Baltic region

Dispersal of alien species is a global problem threatening native biodiversity. Co-introduction of non-native parasites and pathogens adds to the severity of this threat, but this indirect impact has received less attention. To shed light on the key factors determining the richness of microorganisms in native and invasive host species, we compared symbiotic (parasitic and epibiotic) communities of gammarids across different habitats and localities along the Baltic coast of Poland. Seven gammarid species, two native and five invasive, were sampled from 16 freshwater and brackish localities. Sixty symbiotic species of microorganisms of nine phyla were identified. This taxonomically diverse species assemblage of symbionts allowed us to assess the effect of host translocation and regional ecological determinants driving assembly richness in the gammarid hosts. Our results revealed that (i) the current assemblages of symbionts of gammarid hosts in the Baltic region are formed by native and co-introduced species; (ii) species richness of the symbiotic community was higher in the native Gammarus pulex than in the invasive hosts, probably reflecting a process of species loss by invasive gammarids in the new area and the distinct habitat conditions occupied by G. pulex and invasive hosts; (iii) both host species and locality were key drivers shaping assembly composition of symbionts, whereas habitat condition (freshwater versus brackish) was a stronger determinant of communities than geographic distance; (iv) the dispersion patterns of the individual species richness of symbiotic communities were best described by Poisson distributions; in the case of an invasive host, the dispersion of the rich species diversity may switch to a right-skewed negative binomial distribution, suggesting a host-mediated regulation process. We believe this is the first analysis of the symbiotic species richness in native and invasive gammarid hosts in European waters based on original field data and a broad range of taxonomic groups including Microsporidia, Choanozoa, Ciliophora, Apicomplexa, Platyhelminthes, Nematoda, Nematomorha, Acanthocephala and Rotifera, to document the patterns of species composition and distribution.

Histopathological survey for parasite groups in Gammarus varsoviensis (Amphipoda)

Invasive non-native amphipods (Crustacea) are becoming a model system in which to explore the impact and diversity of invasive parasites-parasites that are carried along an invasion route with their hosts. Gammarus varsoviensis is a freshwater amphipod species that has a recently explored invasion history. We provide a histopathological survey for a putatively invasive non-native population of this amphipod, identifying 8 symbiotic groups: Acanthocephala, Rotifera, Digenea, ciliated protozoa, Haplosporidia, Microsporidia, 'Candidatus Aquirickettsiella', and a putative nudivirus, at various prevalence. Our survey indicates that the parasites have no sex bias and that each has the potential to be carried in either sex along an invasion route. We discuss the pathology and prevalence of the above symbiotic groups and whether those that are parasitic may pose a risk if G. varsoviensis were to carry them to novel locations.

Pathology and genetic connectedness of the mangrove crab (Aratus pisonii) – a foundation for understanding mangrove disease ecology

Mangrove forests are productive ecosystems, acting as a sink for CO2, a habitat for a diverse array of terrestrial and marine species, and as a natural barrier to coastline erosion. The species that reside within mangrove ecosystems have important roles to play, including litter decomposition and the recycling of nutrients. Crustacea are important detritivores in such ecosystems and understanding their limitations (i.e. disease) is an important endeavour when considering the larger ecological services provided.

Histology and metagenomics were used to identify viral (Nudiviridae, Alphaflexiviridae), bacterial (Paracoccus sp., 'Candidatus Gracilibacteria sp.’, and Pseudoalteromonas sp.), protozoan, fungal, and metazoan diversity that compose the symbiome of the mangrove crab, Aratus pisonii. The symbiotic groups were observed at varying prevalence under histology: nudivirus (6.5%), putative gut epithelial virus (3.2%), ciliated protozoa (35.5%), gonad fungus (3.2%), gill ectoparasitic metazoan (6.5%). Metagenomic analysis of one specimen exhibiting a nudivirus infection provided the complete host mitochondrial genome (15,642 bp), nudivirus genome (108,981 bp), and the genome of a Cassava common mosaic virus isolate (6387 bp). Our phylogenetic analyses group the novel nudivirus with the Gammanudivirus and protein similarity searches indicate that Carcinus maenas nudivrius is the most similar to the new isolate. The mitochondrial genome were used to mine short fragments used in population genetic studies to gauge an idea of diversity in this host species across the USA, Caribbean, and central and southern America.

This study report several new symbionts based on their pathology, taxonomy, and genomics (where available) and discuss what effect they may have on the crab population. The role of mangrove crabs from a OneHealth perspective were explored, since their pathobiome includes cassava-infecting viruses. Finally, given that this species is abundant in mangrove forests and now boasts a well-described pathogen profile, we posit that A. pisonii is a valuable model system for understanding mangrove disease ecology.

'Candidatus Mellornella promiscua' n. gen. n. sp. (Alphaproteobacteria: Rickettsiales: Anaplasmataceae): an intracytoplasmic, hepatopancreatic, pathogen of the flatback mud crab, Eurypanopeus depressus

Bacterial pathogens are a long-standing threat to the longevity and survival of crustacean hosts. Their presence and continuing emergence require close monitoring to understand their impact on fished, cultured, and wild crustacean populations. We describe a new bacterial pathogen belonging to the Anaplasmataceae family (Alphaproteobacteria: Rickettsiales), providing pathological, ultrastructural, phylogenetic, and genomic evidence to determine a candidate genus and species ('Candidatus Mellornella promiscua'). This bacterium was found to infect the mud crab, Eurypanopeus depressus, on the North Carolina coastline (USA) at a prevalence of 10.8%. 'Candidatus Mellornella promiscua' was often observed in co-infection with the rhizocephalan barnacle, Loxothylacus panopaei. The bacterium was only found in the hepatopancreas of the mud crab host, causing cytoplasmic hypertrophy, tubule necrosis, large plaques within the cytoplasm of the host cell, and an abundance of sex-pili. The circular genome of the bacterium is 1,013,119bp and encodes 939 genes in total. Phylogenetically, the new bacterium branches within the Anaplasmataceae. The genome is dissimilar from other described bacteria, with 16S gene similarity observed at a maximum of 85.3% to a Wolbachia endosymbiont. We explore this novel bacterial pathogen using genomic, phylogenetic, ultrastructural, and pathological methods, discussing these results in light of current bacterial taxonomy, similarity to other bacterial pathogens, and the potential impact upon the surrounding disease ecology of the host and benthic ecosystem.

Cellular Immune Response of an Endemic Lake Baikal Amphipod to Indigenous Pseudomonas sp

Studies of invertebrates have shown that the internal environment of crustaceans is not always sterile in normal conditions, and in many species, it can be populated by microorganisms even in the absence of any visible pathological processes in the body. This observation raises the question of whether genetically modified indigenous hemolymph microorganisms can be used for biotechnological purposes inside the crustacean either as local producers of some compounds or as sensors to physiological parameters. In this study, we tested the ability of the bacteria isolated from the hemolymph of the amphipod Eulimnogammarus verrucosus to hide from the cellular immune response of the host as the most important feature for their potential long-term application in vivo. 16S rDNA amplicon sequencing revealed five common bacterial genera in all analyzed samples of the amphipod hemolymph, among which Pseudomonas is most easily subjected to genome modification and, thus, the most prospective for biotechnological application. Cultivation of Pseudomonas gave us a number of strains undoubtedly derived from the amphipod hemolymph, and one of them (belonging to the Pseudomonas fluorescens group) was chosen for further tests. The primary culture of amphipod hemocytes was used to analyze the immunogenicity of the strain and showed a pronounced reaction of the immune cells to a high amount of the bacteria within six hours. This result indicates that modulation of cellular immune response to metabolically active bacterial cells is not mandatory for the survival and wide distribution of these microorganisms in the hemolymph of numerous amphipod individuals.

Invasive Non-Native Crustacean Symbionts: Diversity and Impact

Invasive non-native species (INNS) pose a risk as vectors of parasitic organisms (Invasive Parasites). Introducing invasive parasites can result in ecological disturbances, leading to biodiversity loss and native species illness/mortality, but occasionally can control INNS limiting their impact. Risks to human health and the economy are also associated with INNS and invasive parasites; however, we understand little about the diversity of symbiotic organisms co-invading alongside INNS. This lack of clarity is an important aspect of the 'One Health' prerogative, which aims to bridge the gap between human, wildlife, and ecosystem health. To explore symbiont diversity associated with the invasive crustacean group (including: crab, lobster, crayfish, shrimp, amphipod, isopod, copepod, barnacle, other) (n = 323) derived from 1054 aquatic invertebrates classed as INNS across databases, we compile literature (year range 1800-2017) from the native and invasive range to provide a cumulative symbiont profile for each species. Our search indicated that 31.2% of INN crustaceans were known to hold at least one symbiont, whereby the remaining 68.8% had no documented symbionts. The symbiont list mostly consisted of helminths (27% of the known diversity) and protists (23% of the known diversity), followed by bacteria (12%) and microsporidians (12%). Carcinus maenas, the globally invasive and extremely well-studied green crab, harboured the greatest number of symbionts (n = 72). Additional screening is imperative to become more informed on invasive symbiont threats. We reveal that few studies provide truly empirical data that connect biodiversity loss with invasive parasites and suggest that dedicated studies on available systems will help to provide vital case studies. Despite the lack of empirical data, co-invasive parasites of invasive invertebrates appear capable of lowering local biodiversity, especially by causing behavioural change and mortality in native species. Alternatively, several invasive parasites appear to protect ecosystems by controlling the impact and population size of their invasive host. We provide a protocol that could be followed to explore symbiont diversity in invasive groups as part of our case studies. The consequence of limited parasite screening of INNS, in addition to the impacts invasive parasites impart on local ecologies, are explored throughout the review. We conclude in strong support of the 'One Health' prerogative and further identify a need to better explore disease in invasion systems, many of which are accountable for economic, human health and ecological diversity impacts.

The Ecological Importance of Amphipod–Parasite Associations for Aquatic Ecosystems

Amphipods are a key component of aquatic ecosystems due to their distribution, abundance and ecological role. They also serve as hosts for many micro- and macro-parasites. The importance of parasites and the necessity to include them in ecological studies has been increasingly recognized in the last two decades by ecologists and conservation biologists. Parasites are able to alter survival, growth, feeding, mobility, mating, fecundity and stressors’ response of their amphipod hosts. In addition to their modulating effects on host population size and dynamics, parasites affect community structure and food webs in different ways: by increasing the susceptibility of amphipods to predation, by quantitatively and qualitatively changing the host diet, and by modifying competitive interactions. Human-induced stressors such as climate change, pollution and species introduction that affect host–parasite equilibrium, may enhance or reduce the infection effects on hosts and ecosystems. The present review illustrates the importance of parasites for ecosystem processes using examples from aquatic environments and amphipods as a host group. As seen from the literature, amphipod–parasite systems are likely a key component of ecological processes, but more quantitative data from natural populations and field evidence are necessary to support the results obtained by experimental research.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

First record of new rickettsia-like organism in the blue king crab Paralithodes platypus from the Sea of Okhotsk: Distribution, morphological evidence and genetic analysis

An infection caused by a rickettsia-like organism (RLO) was detected in the blue king crab Paralithodes platypus from the eastern Sea of Okhotsk. The external signs of the disease are lethargy and an empty gastrointestinal tract. Dissection of infected individuals revealed that their hepatopancreas was light yellow in color. The causative agent of infection is Gram-negative rod-shaped bacterium targeted exclusively at hepatopancreas tissues. In the cytoplasm of infected cells, the bacteria are enclosed in parasite vacuoles or located immediately in cytosol. An ultrastructural analysis showed two main morphological types corresponding to the life cycle stages in the RLO: the vegetative stage of intermediate bodies, characterized by growth and division processes, and the infection stage of elementary bodies, which are spore-like non-dividing short rods surrounded by a multilayered membrane and having an osmiophilic inclusion body. At the terminal stage of infection, as a result of lysis of the infected cells, the RLO enters the lumen of the hepatopancreatic tubules which contributes to the spread of infection. According to genetic analysis based on 16S rRNA gene sequences, the RLO from P. platypus is most closely related to the Candidatus Hepatobacter penaei, NCBI #JX981946 (94.7% similarity) and NCBI #KY363553 (94.1% similarity). The high level of genetic differences (more than 5%) of the studied pathogen, along with the structural features, allows characterizing the RLO isolated from P. platypus as a new species of the genus Candidatus Hepatobacter paralithodi nov. sp., NCBI #MK928971.

Biological denitrification using polycaprolactone-peanut shell as slow-release carbon source treating drainage of municipal WWTP

The development of slow-release carbon source is an effective way to reduce the total nitrogen (TN) in low carbon to nitrogen ratio wastewater. In this study, a novel solid slow-release carbon source (PPP) was prepared using polycaprolactone (PCL) and peanut shell (PS) as carbon sources with polyvinyl alcohol-sodium alginate (PVA-SA) as hybrid scaffolds. The carbon release properties of PPP and each carbon source materials were compared. The performances of nitrogen removal and microbial community structure using PPP as external carbon source were investigated. The results showed that PPP had the best slow-release performance, and its release process followed the first-order release equation. The ratio of acetic acid, propionic acid and butyric acid in released organic matter was stable at (75.73 ± 4.62)%:(17.22 ± 4.53)%:(7.06 ± 1.02)%. When using PPP as an external carbon source for denitrification, the relative abundance of Gammaproteobacteria increased from 39.32% to 46.66%, while the Shannon index decreased from 8.59 to 8.29. The utilization efficiency of PPP was determined by the ratio of the organic matter releasing rate to the released organic matter consumption rate. By optimizing the PPP dosage, both high nitrogen removal efficiency and low residual organic matter could be achieved.

The mitochondrial genome of UK (non-native) Dikerogammarus haemobaphes (Amphipoda: Gammaridae) informs upon Dikerogammarus evolution, invasions and associated microparasites

The amphipod Dikerogammarus haemobaphes is a high-risk carrier of parasites that impact wildlife in its non-native range. Studies using the mitochondrial genes, Cytochrome Oxidase Sub-Unit 1 (cox1) and small-subunit ribosomal RNA gene (16S), provide some nucleotide detail for understanding the evolution and phylogeography of this species. Despite this, the origins of the invasion remain unknown, as do the origins of its parasites. This study provides the full annotated mitochondrial genome (15,460 bp) of D. haemobaphes, consisting of 2 rRNAs, 24 tRNAs and 14 protein coding genes. Mitochondrial genes from the UK isolate are compared to existing data on NCBI and are used in a concatenated phylogenetic approach and identify D. haemobaphes as an early member of the Gammaridae (Amphipoda). Viral, bacterial, protistan and microsporidian parasites are present across the Gammaridae, including D. haemobaphes, suggesting the ancestor of the Gammaridae harboured related diseases, and that further screening of amphipods is likely to reveal further microparasite diversity. This correlation suggests that other gammarid invaders have the potential to harbour a range of microparasites. The mitochondrial genome of this species will act a resource to facilitate our understanding of geneflow, disease epidemiology and evolutionary history in this invasion-disease model.

Pathogens and other symbionts of the Amphipoda: taxonomic diversity and pathological significance

With over 10000 species of Amphipoda currently described, this order is one of the most diverse groups of freshwater and marine Crustacea. Members of this group are globally distributed, and many are keystone species and ecosystem engineers within their respective ecologies. As with most organisms, disease is a key factor that can alter population size, behaviour, survival, invasion potential and physiology of amphipod hosts. This review explores symbiont diversity and pathology in amphipods by coalescing a range of current and historical literature to provide the first full review of our understanding of amphipod disease. The review is broken into 2 parts. The first half explores amphipod microparasites, which include data pertaining to viruses, bacteria, fungi, oomycetes, microsporidians, dinoflagellates, myxozoans, ascetosporeans, mesomycetozoeans, apicomplexans and ciliophorans. The second half reports the metazoan macroparasites of Amphipoda, including rotifers, trematodes, acanthocephalans, nematodes, cestodes and parasitic Crustacea. In all cases we have endeavoured to provide a complete list of known species that cause disease in amphipods, while also exploring the effects of parasitism. Although our understanding of disease in amphipods requires greater research efforts to better define taxonomic diversity and host effects of amphipod symbionts, research to date has made huge progress in cataloguing and experimentally determining the effects of disease upon amphipods. For the future, we suggest a greater focus on developing model systems that use readily available amphipods and diseases, which can be comparable to the diseases in other Crustacea that are endangered, economically important or difficult to house.

The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae

Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.

The Importance of Revisiting Legionellales Diversity

Bacteria of the order Legionellales, such as Legionella pneumophila, the agent of Legionnaires' disease, and Coxiella burnetii, the agent of Q fever, are widely recognized as human pathogens. While our view of the Legionellales is often limited to clinical isolates, ecological surveys are continually uncovering new members of the Legionellales that do not fall into the recognized pathogenic species. Here we emphasize that most of these Legionellales are nonpathogenic forms that have evolved symbiotic lifestyles with nonvertebrate hosts. The diversity of nonpathogenic forms remains, however, largely underexplored. We conjecture that its characterization, once contrasted with the data on pathogenic species, will reveal novel highlights on the mechanisms underlying lifestyle transitions of intracellular bacteria, including the emergence of pathogenesis and mutualism, transmission routes, and host specificity.