Absence of microorganisms in crustacean digestive tracts

Comparative study of the hemolymph microbiome between live and recently dead American lobsters Homarus americanus

Lobsters and other crustaceans do not have sterile hemolymph. Despite this, little is known about the microbiome in the hemolymph of the lobster Homarus americanus. The purpose of this study was to characterize the hemolymph microbiome in lobsters. The lobsters were part of a larger study on the effect of temperature on epizootic shell disease, and several died during the course of the study, providing an opportunity to examine differences in the microbiomes between live and recently dead (1-24 h) animals. The hemolymph microbiomes of live lobsters was different from those in dead animals and both were different from the tank microbiome in which the animals had been held. The microbiomes of live lobsters were more diverse and had a different suite of bacteria than those from dead animals. The dominant taxa in live lobsters belonged to Flavobacteriaceae and Rhodobacteraceae, whereas Vibrionaceae and Enterobacteriaceae were predominant in the dead lobsters. Although aquarium microbiomes overlapped with the hemolymph microbiomes, there was less overlap and lower abundance of taxa in comparison with hemolymph from live lobsters. Previous studies reporting bacteria in the digestive tract of lobsters suggested that Vibrionaceae and Enterobacteriaceae had invaded the hemolymph via the gut. Our study suggests that hemolymph bacteria abundant in live lobsters do not originate from the tank milieu and comprise a rich, natural, or native background of bacterial constituents.

Not all animals need a microbiome

It is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimally or facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several ‘microbiome-free’ lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. We call for further research on microbiome-free taxa to provide a more complete understanding of the ecology and evolution of macrobe-microbe interactions.

Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans

Woody (lignocellulosic) plant biomass is an abundant renewable feedstock, rich in polysaccharides that are bound into an insoluble fiber composite with lignin. Marine crustacean woodborers of the genus Limnoria are among the few animals that can survive on a diet of this recalcitrant material without relying on gut resident microbiota. Analysis of fecal pellets revealed that Limnoria targets hexose-containing polysaccharides (mainly cellulose, and also glucomannans), corresponding with the abundance of cellulases in their digestive system, but xylans and lignin are largely unconsumed. We show that the limnoriid respiratory protein, hemocyanin, is abundant in the hindgut where wood is digested, that incubation of wood with hemocyanin markedly enhances its digestibility by cellulases, and that it modifies lignin. We propose that this activity of hemocyanins is instrumental to the ability of Limnoria to feed on wood in the absence of gut symbionts. These findings may hold potential for innovations in lignocellulose biorefining.

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion

The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source.

DOI:http://dx.doi.org/10.7554/eLife.20062.001

The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory.

Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available.

Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases.

Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production.

DOI:http://dx.doi.org/10.7554/eLife.20062.002

Bacteria associated with Artemia spp. along the salinity gradient of the solar salterns at Eilat (Israel)

The crustacean genus Artemia naturally inhabits various saline and hypersaline environments and is the most frequently laboratory-hatched animal for live feed in mari- and aquaculture. Because of its high economic importance, Artemia-bacteria interactions were so far studied mostly in laboratory strains. In this study, we focused our attention on the Artemia-associated microbiota in its natural environment in the solar salterns of Eilat, Israel. We applied a culture-independent method (clone libraries) to investigate the bacterial community structure associated with Artemia in five evaporation ponds with salinities from slightly above seawater (5%) to the point of saturation (32%), in two different developmental stages: in nauplii and in the intestine of adult animals. Bacteria found in naupliar and adult stages were classified within the Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Cyanobacteria. The halophilic proteobacterial genera Halomonas spp. and Salinivibrio spp. dominated the Artemia microbiota in both stages in all ponds. We also analysed a clone library of entire adult animals, revealing a novel bacterial phylogenetic lineage. This is the first molecular study of bacteria associated with two developmental stages of Artemia along a salinity gradient.

Isolation of a deep-sea barophilic bacterium and some of its growth characteristics

A bacterium, a spirillum, has been isolated from a deep-sea sample and has been found to grow optimally at about 500 bars and 2 degrees to 4 degrees C. These conditions are similar to those prevailing at the 5700-meter depth from which the sample was collected. The organism grows at these pressures and temperatures with a generation time of between 4 and 13 hours; at atmospheric pressure and 2 degrees to 4 degrees C, the generation time is about 3 to 4 days.

Bacteria associated with the surface and gut of marine copepods

Little is known about the nature of bacteria associated with the surface and gut of marine copepods, either in laboratory-reared animals or in the natural environment. Nor is it known whether such animals possess a gut flora. The present report deals with studies of microorganisms isolated from healthy, laboratory-reared copepods of the species Acartia tonsa Dana, from several species of wild copepods collected from a marine or estuarine environment, and from laboratory dishes containing moribund copepods. Evidence for a unique gut flora in laboratory-reared animals is presented; the predominant bacteria were represented by the genus Vibrio. Other organisms such as Pseudomonas and Cytophaga were found less abundantly associated with the copepods and not specifically associated with the gut.

Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes

The digestion of lignocellulose is attracting attention both in terms of basic research into its metabolism by microorganisms and animals, and also as a means of converting plant biomass into biofuels. Limnoriid wood borers are unusual because, unlike other wood-feeding animals, they do not rely on symbiotic microbes to help digest lignocellulose. The absence of microbes in the digestive tract suggests that limnoriid wood borers produce all the enzymes necessary for lignocellulose digestion themselves. In this study we report that analysis of ESTs from the digestive system of Limnoria quadripunctata reveals a transcriptome dominated by glycosyl hydrolase genes. Indeed, > 20% of all ESTs represent genes encoding putative cellulases, including glycosyl hydrolase family 7 (GH7) cellobiohydrolases. These have not previously been reported in animal genomes, but are key digestive enzymes produced by wood-degrading fungi and symbiotic protists in termite guts. We propose that limnoriid GH7 genes are important for the efficient digestion of lignocellulose in the absence of gut microbes. Hemocyanin transcripts were highly abundant in the hepatopancreas transcriptome. Based on recent studies indicating that these proteins may function as phenoloxidases in isopods, we discuss a possible role for hemocyanins in lignin decomposition.

Peritrophic membrane of the penaeid shrimp Sicyonia ingentis: structure, formation, and permeability

Peritrophic membranes (PTMs) are secreted acellular layers that separate ingested materials from the gut epithelium in a variety of invertebrates. In insects and crustaceans, PTMs are produced in the midgut trunk (MGT, or intestine), but the MGT in decapod crustaceans, unlike that of insects, is not involved with digestion or absorption of food. We demonstrate that the PTM in the penaeid shrimp Sicyonia ingentis is similar to that in other crustaceans that have been studied and is primarily composed of chitin. The lectin WGA binds only to the PTM and glycocalyx along the microvilli of the midgut cells, which is consistent with the suggestion that the chitin is synthesized along the microvilli. The PTM is only permeable to inert particles smaller than 20 nm. We also describe the secretion of granules, which fill the apices of the epithelial cells, into the ectoperitrophic space. Although their function is not clear, they do not contribute to the PTM.

Nutrition in terrestrial isopods (Isopoda: Oniscidea): an evolutionary-ecological approach

The nutritional morphology, physiology and ecology of terrestrial isopods (Isopoda: Oniscidea) is significant in two respects. (1) Most oniscid isopods are truly terrestrial in terms of being totally independent of the aquatic environment. Thus, they have evolved adaptations to terrestrial food sources. (2) In many terrestrial ecosystems, isopods play an important role in decomposition processes through mechanical and chemical breakdown of plant litter and by enhancing microbial activity. While the latter aspect of nutrition is discussed only briefly in this review, I focus on the evolutionary ecology of feeding in terrestrial isopods. Due to their possessing chewing mouthparts, leaf litter is comminuted prior to being ingested, facilitating both enzymatic degradation during gut passage and microbial colonization of egested faeces. Digestion of food through endogenous enzymes produced in the caeca of the midgut glands (hepatopancreas) and through microbial enzymes, either ingested along with microbially colonized food or secreted by microbial endosymbionts, mainly takes place in the anterior part of the hindgut. Digestive processes include the activity of carbohydrases, proteases, dehydrogenases, esterases, lipases, arylamidases and oxidases, as well as the nutritional utilization of microbial cells. Absorption of nutrients is brought about by the hepatopancreas and/or the hindgut epithelium, the latter being also involved in osmoregulation and water balance. Minerals and metal cations are effectively extracted from the food, while overall assimilation efficiencies may be low. Heavy metals are stored in special organelles of the hepatopancreatic tissue. Nitrogenous waste products are excreted via ammonia in its gaseous form, with only little egested along with the faeces. Nonetheless, faeces are characterized by high nitrogen content and provide a favourable substrate for microbial colonization and growth. The presence of a dense microbial population on faecal material is one reason for the coprophagous behaviour of terrestrial isopods. For the same reason, terrestrial isopods prefer feeding on decaying rather than fresh leaf litter, the former also being more palatable and easier to digest. Acceptable food sources are detected through distance and contact chemoreceptors. The 'quality' of the food source determines individual growth, fecundity and mortality, and thus maintenance at the population level. Due to their physiological adaptations to feeding on and digesting leaf litter, terrestrial isopods contribute strongly to nutrient recycling during decomposition processes. Yet, many of these adaptations are still not well understood.

Epibiotic microorganisms on copepods and other marine crustaceans

Although the occurrence of microbial (algal, protozoan, bacterial, and fungal) epibionts on marine crustaceans and other invertebrates has been documented repeatedly, the ecological context and significance of these relationships generally are not well understood. Recently, several studies have examined the population and community ecology of algal and protozoan epibionts on freshwater crustaceans. Even so, the study of microbial epibionts in aquatic environments is still in its infancy. In this review, we summarize associations of microalgae, protozoans, and bacteria with marine crustaceans, especially copepods. We note differences and commonalities across epibiont taxa, consider host-epibiont cycling of nutrients, generate hypotheses relevant to the ecology of the host and the epibiont, and suggest future research opportunities.

Gut microflora of two saltmarsh detritivore thalassinid prawns,Upogebia africana andCallianassa kraussi

The presence and digestive capabilities of bacteria associated with the digestive systems and habitats of two saltmarsh-burrowing detritivore thalassinid prawns (Upogebia africana andCallianassa kraussi) was examined.U. africana is a filter-feeding prawn inhabiting muddy deposits, whereasC. kraussi, a deposit feeder, inhabits coarser more sandy deposits. Scanning electron microscopy was used to examine the gut lining and associated microflora and the nature of the ingested food of both prawns. The gut contents of both prawns included plant fragments, fragmented diatoms, partially degraded protozoa, and bacteria attached to organic matter. In bothU. africana andC. kraussi the midgut walls and gut contents were extensively coated by filamentous bacteria which were absent in the hindgut. The hindgut epithelium ofU. africana was coated by mats of rodshaped bacteria, not reported in marine invertebrates previously. The digestive glands of both species contained bacteria in the lumen. Isolation of gut and habitat bacteria suggests that bothU. africana andC. kraussi maintain a gut microflora distinct from the habitat microflora. Bacteria isolated from the guts of both species of prawn differed from those isolated from their respective habitats with regards to both the genera isolated and their digestive capabilities. The dominant genera isolated from the guts of bothU. africana andC. kraussi wereVibrio andPseudomonas, with an unidentified fermenter andPseudomonas, respectively dominating in the digestive glands. Bacteria of the genusAcinetobacter dominated the isolates from the habitats of both species of prawn. Resident gut bacteria isolated from the guts of both species of prawn exhibited lipase, protease, chitinase, and lysozyme, but not cellulase activity, and may contribute to nitrogen aquisition by the prawns. Isolates from the prawns' habitat exhibited alginase, gelatinase, and lipase activity, a few (3%) fromU. africana habitat having cellulases. In this study a distinction between resident gut bacteria and transient gut bacteria was made. Results suggest that some habitat bacteria remain viable in the guts ofU. africana, but not inC. kraussi.

Isolation of a bacterium resembling Pirellula species from primary tissue culture of the giant tiger prawn (Penaeus monodon)

During attempts to establish tissue cultures from hepatopancreas, heart, and hemolymph of the giant tiger prawn (Penaeus monodon), using a medium including penicillin, streptomycin, and amphotericin B, bacterial contamination in the form of a sheet of growth attached to the tissue culture vessel was a persistent problem. Contaminant bacteria were teardrop-shaped cells arranged in rosettes, and electron microscopy revealed buds, crateriform structures, and the absence of a peptidoglycan layer in the cell wall, features characteristic of bacteria in the Planctomyces-Pirellula group, a phylogenetically distinct group of eubacteria. Two strains of contaminant bacteria were isolated in pure culture. Both exhibited morphology and antibiotic resistance consistent with their membership in the Planctomyces-Pirellula group (order Planctomycetales) of eubacteria. Tissue culture media for marine invertebrates may select for such bacteria if high concentrations of cell wall synthesis-inhibiting antibiotics are included.

Absence of surface-associated microorganisms in adult oysters (Crassostrea gigas)

Healthy, actively feeding intertidal oysters were removed from an estuarine environment (Pipeclay Lagoon, Tasmania). The epithelial surfaces of various organs of the mantle cavity and alimentary tract were explored by scanning and transmission electron microscopy. All epithelial tissues examined were ciliated, and nearly all were partly covered with secreted mucus. However, microorganisms were seen rarely in the adhesive mucus and never attached to the epithelium. Electron microscopy also failed to demonstrate a surface microflora in emersed oysters which had been incubated at 5 to 25 degrees C for 6 or 24 h. The absence of an internal surface microflora did not vary on a seasonal basis. In laboratory experiments, oysters were allowed to filter feed from seawater containing diverse types of marine bacteria at concentrations of 10(3) to 10(7)/mL. However, no surface microflora could be found within actively feeding oysters or in emersed animals incubated at 20 degrees C for 6 or 24 h. In contrast, surface-associated microorganisms were detected readily by scanning electron microscopy on the external shell of healthy oysters and on various internal tissues in spoiled oysters. It is suggested that the major mechanisms restricting microbial growth within oysters are ciliary movement and mucus secretion.

External Microflora of a Marine Wood-Boring Isopod

Bacteria associated with the marine wood-boring isopod Limnoria lignorum were enumerated by acridine orange epifluorescence microscopy and by plate counts on several media; the plate-viable bacteria were isolated and identified. Similar procedures were followed to enumerate and identify bacteria associated with the wood substrate from which the isopods were collected and with the surrounding water from the isopod habitat. Approximately 1.4 × 10 7 bacterial cells were associated with each individual L. lignorum. Aeromonas hydrophila, Pseudomonas , and Vibrio were the most common genera in the isopod microflora. Wood from L. lignorum burrows had an associated bacterial flora of 1.6 × 10 7 cells per mg (damp weight). A. hydrophila also predominated in the wood microflora. The water from which the isopod population was collected contained 2.3 × 10 6 bacteria per ml. Pseudomonas and Vibrio species were very common in the water microflora, but A. hydrophila was not detected. Interactions between the isopod, its associated microorganisms, and the microorganisms within the wood substrate are discussed in the light of the known absence of a resident digestive tract microflora in these animals.