Acidovorax-like symbionts in the nephridia of earthworms

Draft Genome of Acidovorax kalamii Strain JM16, Isolated from Skin Mucus of Zebrafish (Danio rerio)

Acidovorax kalamii strain JM16 was isolated from the skin mucus of the zebrafish, Danio rerio. Its genome is 5.3 Mb with a 65.6% GC content and encodes quorum sensing capabilities, which could contribute to ecosystem functioning within the fish host skin bacterial community.

Fe(II) Addition Drives Soil Bacterial Co-Ocurrence Patterns and Functions Mediated by Anaerobic and Chemoautotrophic Taxa

Iron is among the most abundant elements in the soil of paddy fields, and its valence state and partitioning can be transformed by flooding and drainage alternations. However, little is known about the function of soil microbes that interact with Fe(II). In this study, sandy and loamy soils originating from rice fields were treated with Fe(II) at low and high concentrations. The findings demonstrate that additional Fe(II) has various effects on the soil’s microbial community structure and metabolic pathways. We conclude that Fe(II) at high concentrations reduced bacterial abundance and diversity in two textured paddy soils, yet the abundance in loamy soils was higher than it was in sandy soil. Additionally, in environments with high Fe(II) levels, the relative abundance of both anaerobic and chemoautotrophic bacteria increased. The Fe(II) concentration was positively correlated with total reduced substances but negatively correlated with redox potential and pH. Co-occurrence networks revealed that Fe(II) significantly promoted interactions with the most anaerobic and chemoautotrophic bacteria. In addition, adding Fe(II) greatly increased the number of more complex bacterial networks, and an increase in the number of mutually beneficial taxa occurred. We found that Fe(II) promoted the methane pathway, the Calvin cycle, and nitrate reduction to small but significant extents. These pathways involve the growth and interrelation of autotrophic and anaerobic bacteria. These results suggest that changes in the bacterial community structure occur in many dry–wet alternating environments.

Taxonomic and functional characteristics of aerobic bacteria isolated from the chloragogenous tissue of the earthworm Aporrectodea molleri

Earthworms are considered as a rich microhabitat for the growth and proliferation of diverse soil microorganisms. Hence, earthworms' associated bacteria attracted interest due to their high metabolic profiles and benefits to soil fertility and plant growth. In this study, we aimed to isolate for the first-time aerobic bacteria present in the chloragogenous tissue of the earthworm Apporectodea molleri and test their Plant Growth-Promoting abilities and their resistance to heavy metals (Mn, Zn, Cu, Cd, and Ni). The 16S rRNA gene sequencing revealed the affiliation of the fifteen isolates to six main bacterial genera: Enterobacter, Citrobacter, Aeromonas, Pseudomonas, Bacillus, Terribacillus. These strains displayed different plant growth promoting traits (e.g., indole-3-acetic acid IAA, siderophores, nitrogen fixation, phosphate, and potassium solubilization), in addition, they were able to resist differently to heavy metals. Bacillus strains were most effective as three strains, namely B. subtilis strain TC34; B. circulans strain TC7 and Bacillus sp. strain TC10, were positive to all PGP traits and resisted to all heavy metals. This study illustrates the potential of bacteria from the chloragogenous tissue to exhibit multiple properties, which can be related to the functional feature of this tissue to stock metabolites and neutralize toxic elements.

Arsenic and the gastrointestinal tract microbiome

Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe-arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value.

The draft genome of a new Verminephrobacter eiseniae strain: a nephridial symbiont of earthworms

Purpose

Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu.

Methods

We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria.

Result

The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search.

Conclusion

The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further.

Pontoscolex corethrurus: A homeless invasive tropical earthworm?

The presence of earthworm species in crop fields is as old as agriculture itself. The earthworms Pontoscolex corethrurus (invasive) and Balanteodrilus pearsei (native) are associated with the emergence of agriculture and sedentism in the region Amazon and Maya, respectively. Both species have shifted their preference from their natural habitat to the cropland niche. They contrast in terms of intensification of agricultural land use (anthropic impact to the symbiotic soil microbiome). P. corethrurus inhabits conventional agroecosystems, while B. pearsei thrives in traditional agroecosystems, i.e., P. corethrurus has not yet been recorded in soils where B. pearsei dwells. The demographic behavior of these two earthworm species was assessed in the laboratory over 100 days, according to their origin (OE; P. corethrurus and B. pearsei) food quality (FQ; soil only, maize stubble, Mucuna pruriens), and soil moisture (SM; 25, 33, 42%). The results showed that OE, FQ, SM, and the OE x FQ interaction were highly significant for the survival, growth, and reproduction of earthworms. P. corethrurus showed a lower survival rate (> mortality). P. corethrurus survivors fed a diet of low-to-intermediate nutritional quality (soil and stubble maize, respectively) showed a greater capacity to grow and reproduce; however, it was surpassed by the native earthworm when fed a high-quality diet (M. pruriens). Besides, P. corethrurus displayed a low cocoon hatching (emergence of juveniles). These results suggest that the presence of the invasive species was associated with a negative interaction with the soil microbiota where the native species dwells, and with the absence of natural mutualistic bacteria (gut, nephridia, and cocoons). These results are consistent with the absence of P. corethrurus in milpa and pasture-type agricultural niches managed by peasants (agroecologists) to grow food regularly through biological soil management. Results reported here suggest that P. corethrurus is an invasive species that is neither wild nor domesticated, that is, its eco-evolutionary phylogeny needs to be derived based on its symbionts.

Distinct effects of the nephridial symbionts Verminephrobacter and Candidatus Nephrothrix on reproduction and maturation of its earthworm host Eisenia andrei

Verminephrobacter, the most common specific symbionts in the nephridia (excretory organs) of lumbricid earthworms, have been shown to improve reproduction of the garden earthworm Aporrectodea tuberculata under nutrient limitation. It is unknown how general this beneficial trait is in the Verminephrobacter-earthworm symbiosis, whether other nephridial symbionts also affect host fitness and what the mechanism of the fitness increase is. Here we report beneficial effects of Verminephrobacter and Candidatus Nephrothrix on life history traits of the compost worm Eisenia andrei, which in addition to these two symbionts also hosts Agromyces-like bacteria in its mixed nephridial community: while growth was identical between control, Verminephrobacter-free and aposymbiotic worms, control worms produced significantly more cocoons and offspring than both Verminephrobacter-free and aposymbiotic worms, confirming the reproductive benefit of Verminephrobacter in a second host with different ecology and feeding behavior. Furthermore, worms with Verminephrobacter and Ca. Nephrothrix, or with only Ca. Nephrothrix present, reached sexual maturity significantly earlier than aposymbiotic worms; this is the first evidence for a beneficial role of Ca. Nephrothrix in earthworms. Riboflavin content in cocoons and whole earthworms was unaffected by the presence or absence of nephridial symbionts, suggesting that nutritional supplementation with this vitamin does not play a major role in this symbiosis.

Cophylogenetic analysis suggests cospeciation between the Scorpion Mycoplasma Clade symbionts and their hosts

Scorpions are predator arachnids of ancient origin and worldwide distribution. Two scorpion species, Vaejovis smithi and Centruroides limpidus, were found to harbor two different Mollicutes phylotypes: a Scorpion Mycoplasma Clade (SMC) and Scorpion Group 1 (SG1). Here we investigated, using a targeted gene sequencing strategy, whether these Mollicutes were present in 23 scorpion morphospecies belonging to the Vaejovidae, Carboctonidae, Euscorpiidae, Diplocentridae, and Buthidae families. Our results revealed that SMC is found in a species-specific association with Vaejovidae and Buthidae, whereas SG1 is uniquely found in Vaejovidae. SMC and SG1 co-occur only in Vaejovis smithi where 43% of the individuals host both phylotypes. A phylogenetic analysis of Mollicutes 16S rRNA showed that SMC and SG1 constitute well-delineated phylotypes. Additionally, we found that SMC and scorpion phylogenies are significantly congruent, supporting the observation that a cospeciation process may have occurred. This study highlights the phylogenetic diversity of the scorpion associated Mollicutes through different species revealing a possible cospeciation pattern.

Diversity, structure and sources of bacterial communities in earthworm cocoons

Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca. Nephrothrix showed a high rate of sequence variation, suggesting that they could be biparentally acquired during mating. The other bacterial species inhabiting the cocoons came from the bedding, where they accounted for a small fraction of the diversity (27% and 7% of bacterial species for E. andrei and E. fetida bedding). Hence, earthworm cocoon microbiome includes a large fraction of the vertically-transmitted symbionts and a minor fraction, but more diverse, horizontally and non-randomly acquired from the environment. These data suggest that horizontally-transmitted bacteria to cocoons may play an important role in the adaptation of earthworms to new environments or diets.

Evolution of the tripartite symbiosis between earthworms, Verminephrobacter and Flexibacter-like bacteria

Nephridial (excretory organ) symbionts are widespread in lumbricid earthworms and the complexity of the nephridial symbiont communities varies greatly between earthworm species. The two most common symbionts are the well-described Verminephrobacter and less well-known Flexibacter-like bacteria. Verminephrobacter are present in almost all lumbricid earthworms, they are species-specific, vertically transmitted, and have presumably been associated with their hosts since the origin of lumbricids. Flexibacter-like symbionts have been reported from about half the investigated earthworms; they are also vertically transmitted. To investigate the evolution of this tri-partite symbiosis, phylogenies for 18 lumbricid earthworm species were constructed based on two mitochondrial genes, NADH dehydrogenase subunit 2 (ND2) and cytochrome c oxidase subunit I (COI), and compared to their symbiont phylogenies based on RNA polymerase subunit B (rpoB) and 16S rRNA genes. The two nephridial symbionts showed markedly different evolutionary histories with their hosts. For Verminephrobacter, clear signs of long-term host-symbiont co-evolution with rare host switching events confirmed its ancient association with lumbricid earthworms, likely dating back to their last common ancestor about 100 million years (MY) ago. In contrast, phylogenies for the Flexibacter-like symbionts suggested an ability to switch to new hosts, to which they adapted and subsequently became species-specific. Putative co-speciation events were only observed with closely related host species; on that basis, this secondary symbiosis was estimated to be minimum 45 MY old. Based on the monophyletic clustering of the Flexibacter-like symbionts, the low 16S rRNA gene sequence similarity to the nearest described species (<92%) and environmental sequences (<94.2%), and the specific habitat in the earthworm nephridia, we propose a new candidate genus for this group, Candidatus Nephrothrix.

The effect of anthropogenic arsenic contamination on the earthworm microbiome

Earthworms are globally distributed and perform essential roles for soil health and microbial structure. We have investigated the effect of an anthropogenic contamination gradient on the bacterial community of the keystone ecological species Lumbricus rubellus through utilizing 16S rRNA pyrosequencing for the first time to establish the microbiome of the host and surrounding soil. The earthworm-associated microbiome differs from the surrounding environment which appears to be a result of both filtering and stimulation likely linked to the altered environment associated with the gut micro-habitat (neutral pH, anoxia and increased carbon substrates). We identified a core earthworm community comprising Proteobacteria (∼50%) and Actinobacteria (∼30%), with lower abundances of Bacteroidetes (∼6%) and Acidobacteria (∼3%). In addition to the known earthworm symbiont (Verminephrobacter sp.), we identified a potential host-associated Gammaproteobacteria species (Serratia sp.) that was absent from soil yet observed in most earthworms. Although a distinct bacterial community defines these earthworms, clear family- and species-level modification were observed along an arsenic and iron contamination gradient. Several taxa observed in uncontaminated control microbiomes are suppressed by metal/metalloid field exposure, including eradication of the hereto ubiquitously associated Verminephrobacter symbiont, which raises implications to its functional role in the earthworm microbiome.

Host demise as a beneficial function of indigenous microbiota in human hosts

The age structure of human populations is exceptional among animal species. Unlike with most species, human juvenility is extremely extended, and death is not coincident with the end of the reproductive period. We examine the age structure of early humans with models that reveal an extraordinary balance of human fertility and mortality. We hypothesize that the age structure of early humans was maintained by mechanisms incorporating the programmed death of senescent individuals, including by means of interactions with their indigenous microorganisms. First, before and during reproductive life, there was selection for microbes that preserve host function through regulation of energy homeostasis, promotion of fecundity, and defense against competing high-grade pathogens. Second, we hypothesize that after reproductive life, there was selection for organisms that contribute to host demise. While deleterious to the individual, the presence of such interplay may be salutary for the overall host population in terms of resource utilization, resistance to periodic diminutions in the food supply, and epidemics due to high-grade pathogens. We provide deterministic mathematical models based on age-structured populations that illustrate the dynamics of such relationships and explore the relevant parameter values within which population viability is maintained. We argue that the age structure of early humans was robust in its balance of the juvenile, reproductive-age, and senescent classes. These concepts are relevant to issues in modern human longevity, including inflammation-induced neoplasia and degenerative diseases of the elderly, which are a legacy of human evolution.

IMPORTANCE

The extended longevity of modern humans is a very recent societal artifact, although it is inherent in human evolution. The age structure of early humans was balanced by fertility and mortality, with an exceptionally prolonged juvenility. We examined the role of indigenous microbes in early humans as fundamental contributors to this age structure. We hypothesize that the human microbiome evolved mechanisms specific to the mortality of senescent individuals among early humans because their mortality contributed to the stability of the general population. The hypothesis that we present provides new bases for modern medical problems, such as inflammation-induced neoplasia and degenerative diseases of the elderly. We postulate that these mechanisms evolved because they contributed to the stability of early human populations, but their legacy is now a burden on human longevity in the changed modern world.

Bacteria-bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance

Epithelial surfaces of most animals are colonized by diverse microbial communities. Although it is generally agreed that commensal bacteria can serve beneficial functions, the processes involved are poorly understood. Here we report that in the basal metazoan Hydra, ectodermal epithelial cells are covered with a multilayered glycocalyx that provides a habitat for a distinctive microbial community. Removing this epithelial microbiota results in lethal infection by the filamentous fungus Fusarium sp. Restoring the complex microbiota in gnotobiotic polyps prevents pathogen infection. Although mono-associations with distinct members of the microbiota fail to provide full protection, additive and synergistic interactions of commensal bacteria are contributing to full fungal resistance. Our results highlight the importance of resident microbiota diversity as a protective factor against pathogen infections. Besides revealing insights into the in vivo function of commensal microbes in Hydra, our findings indicate that interactions among commensal bacteria are essential to inhibit pathogen infection.

The earthworm-Verminephrobacter symbiosis: an emerging experimental system to study extracellular symbiosis

Almost all Lumbricid earthworms (Oligochaeta: Lumbricidae) harbor extracellular species-specific bacterial symbionts of the genus Verminephrobacter (Betaproteobacteria) in their nephridia. The symbionts have a beneficial effect on host reproduction and likely live on their host's waste products. They are vertically transmitted and presumably associated with earthworms already at the origin of Lumbricidae 62–136 million years ago. The Verminephrobacter genomes carry signs of bottleneck-induced genetic drift, such as accelerated evolutionary rates, low codon usage bias, and extensive genome shuffling, which are characteristic of vertically transmitted intracellular symbionts. However, the Verminephrobacter genomes lack AT bias, size reduction, and pseudogenization, which are also common genomic hallmarks of vertically transmitted, intracellular symbionts. We propose that the opportunity for genetic mixing during part of the host—symbiont life cycle is the key to evade drift-induced genome erosion. Furthermore, we suggest the earthworm-Verminephrobacter association as a new experimental system for investigating host-microbe interactions, and especially for understanding genome evolution of vertically transmitted symbionts in the presence of genetic mixing.

Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics

The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO₂ fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi.

Assessment of bacterial diversity during composting of agricultural byproducts

Background

Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts.

Results

The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 10⁵ to 10⁹ cfu g^-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts.

Conclusion

The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost. These bacteria can be used as potential compost inoculants for accelerating composting process.

Methylation of mercury in earthworms and the effect of mercury on the associated bacterial communities

Methylmercury compounds are very toxic for most organisms. Here, we investigated the potential of earthworms to methylate inorganic-Hg. We hypothesized that the anaerobic and nutrient-rich conditions in the digestive tracts of earthworm's promote the methylation of Hg through the action of their gut bacteria. Earthworms were either grown in sterile soils treated with an inorganic (HgCl₂) or organic (CH₃HgCl) Hg source, or were left untreated. After 30 days of incubation, the total-Hg and methyl-Hg concentrations in the soils, earthworms, and their casts were analyzed. The impact of Hg on the bacterial community compositions in earthworms was also studied. Tissue concentrations of methyl-Hg in earthworms grown in soils treated with inorganic-Hg were about six times higher than in earthworms grown in soils without Hg. Concentrations of methyl-Hg in the soils and earthworm casts remained at significantly lower levels suggesting that Hg was mainly methylated in the earthworms. Bacterial communities in earthworms were mostly affected by methyl-Hg treatment. Terminal-restriction fragments (T-RFs) affiliated to Firmicutes were sensitive to inorganic and methyl-Hg, whereas T-RFs related to Betaproteobacteria were tolerant to the Hg treatments. Sulphate-reducing bacteria were detected in earthworms but not in soils.

A global survey of the bacteria within earthworm nephridia

Earthworms comprise 16 described families in the Crassiclitellata plus a few other minor groups. Microscopy studies of the early 20th century detected bacteria within the excretory organs, the nephridia, of species within a few of these families. More recent evidence for the consistent and specific association of bacteria with nephridia within the Lumbricidae has been well documented, but the presence and identity of nephridial bacteria among the rest of the Crassiclitellata families had not been explored. The study presented here aimed to identify members of Crassiclitellata families that harbor bacteria in their nephridia, and identify these bacteria based on 16S rRNA gene sequences. Eleven earthworm families were surveyed from countries of six continents, and two island nations. The results revealed members of four bacterial orders commonly occurred within nephridia of genera within nine Crassiclitellata families. Members of the bacterial phyla Bacteroidetes (order Sphingobacteriales), Betaproteobacteria (order Burkholderiales; family Comamonadaceae), and Alphaproteobacteria (orders Rhodospirillales and Rhizobiales) were detected in the nephridia of basal Crassiclitellata, as well as in derived families. Earthworm genera with meronephridia, multiple small nephridia per segment, lacked bacteria, whereas bacteria were often detected in holonephridia, single pairs of large nephridia with a distinct morphology and external excretory pore. The Acanthodrilidae members, a large derived family of earthworms, did not appear to possess nephridial bacteria regardless of nephridial form. Although earthworms from a variety of habitat types were sampled, there were no clear correlations of lifestyle with symbiont types, with the exception of the aquatic earthworms that contained bacteria unrelated to those in any other earthworms. The findings support an evolutionarily long association of bacteria within the Crassiclitellata, and suggest a contribution to nitrogen conservation for the earthworms.

16S rDNA-based metagenomic analysis of bacterial diversity associated with two populations of the kleptoplastic sea slug Elysia chlorotica and its algal prey Vaucheria litorea

The molluscan sea slug Elysia chlorotica is best known for its obligate endosymbiosis with chloroplasts (= kleptoplasty) from its algal prey Vaucheria litorea and its ability to sustain itself photoautotrophically for several months. This unusual photosynthetic sea slug also harbors an array of undescribed bacteria, which may contribute to the long-term success of the symbiosis. Here, we utilized 16S rDNA-based metagenomic analyses to characterize the microbial diversity associated with two populations of E. chlorotica from Halifax, Nova Scotia, Canada, and from Martha's Vineyard, Massachusetts, USA. Animals were examined immediately after collection from their native environments, after being starved of their algal prey for several months, and after being bred in the laboratory (second-generation sea slugs) to characterize the effect of varying environmental and culturing conditions on the associated bacteria. Additionally, the microbiome of the algal prey, laboratory-cultured V. litorea, was analyzed to determine whether the laboratory-bred sea slugs obtained bacteria from their algal food source during development. Bacterial profiles varied between populations and among all conditions except for the F2 laboratory-bred samples, which were similar in diversity and abundance, but not to the algal microbiome. Alpha-, beta-, and gamma-proteobacteria dominated all of the samples along with Actinobacteria, Bacilli, Flavobacteria, and Sphingobacteria. Bacteria capable of polysaccharide digestion and photosynthesis, as well as putative nitrogen fixation, vitamin B(12) production, and natural product biosynthesis were associated with the sea slug and algal samples.

Verminephrobacter eiseniae type IV pili and flagella are required to colonize earthworm nephridia

The bacterial symbiont Verminephrobacter eiseniae colonizes nephridia, the excretory organs, of the lumbricid earthworm Eisenia fetida. E. fetida transfers V. eisenia into the egg capsule albumin during capsule formation and V. eiseniae cells migrate into the earthworm nephridia during embryogenesis, where they bind and persist. In order to characterize the mechanistic basis of selective tissue colonization, methods for site-directed mutagenesis and colonization competence were developed and used to evaluate the consequences of individual gene disruptions. Using these newly developed tools, two distinct modes of bacterial motility were shown to be required for V. eiseniae colonization of nascent earthworm nephridia. Flagella and type IV pili mutants lacked motility in culture and were not able to colonize embryonic earthworms, indicating that both twitching and flagellar motility are required for entrance into the nephridia.

Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms

While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60–130 Myr) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it with the genomes of Verminephrobacter eiseniae and two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A–T bias. We characterized the strength of purifying selection (ω = dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (ω = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher ω values and less codon usage bias in symbiont compared with reference genomes. Relaxation was not evenly distributed among functional gene categories but was overrepresented in genes involved in signal transduction and cell envelope biogenesis. The same gene categories also harbored instances of positive selection in the Verminephrobacter clade. In total, positive selection was detected in 89 genes, including also genes involved in DNA metabolism, tRNA modification, and TonB-dependent iron uptake, potentially highlighting functions important in symbiosis. Our results suggest that the transition to symbiosis was accompanied by molecular adaptation, while purifying selection was only moderately relaxed, despite the evolutionary age and stability of the host association. We hypothesize that biparental transmission of symbionts and rare genetic mixing during transmission can prevent genome erosion in heritable symbionts.

Verminephrobacter aporrectodeae sp. nov. subsp. tuberculatae and subsp. caliginosae, the specific nephridial symbionts of the earthworms Aporrectodea tuberculata and A. caliginosa

Clone library-based studies have shown that almost all lumbricid earthworm species harbour host-specific symbiotic bacteria belonging to the novel genus Verminephrobacter in their nephridia (excretory organs). To date the only described representative from this genus is Verminephrobacter eiseniae, the specific symbiont of the earthworm Eisenia fetida. In this study two novel rod-shaped, non-endosporeforming, betaproteobacterial symbionts were isolated from the nephridia of two closely related earthworm species. Both isolates were affiliated with the genus Verminephrobacter by 16S rRNA gene sequence analysis. Similarly to V. eiseniae, the two isolates grew aerobically with a preference for low oxygen concentrations on a range of sugars, fatty acids and amino acids and fermentatively on glucose and pyruvate. These phenotypes match well with the conditions reported or inferred for the nephridial environment. Based on 16S rRNA gene similarity, DNA-DNA hybridization value and phenotypic characteristics the two isolates are clearly distinct from V. eiseniae. Phenotypic characteristics could not clearly differentiate the two strains as separate species but a low DNA-DNA hybridization value of 57.3%, their earthworm host specificity, differing temperature ranges and pH optima suggest that they represent two subspecies of a novel species of Verminephrobacter. For this species, the name V. aporrectodeae sp. nov. is proposed, with the two subspecies V. aporrectodeae subsp. tuberculatae (type strain, At4(T) = DSM 21361(T) = LMG 25313(T)) and V. aporrectodeae subsp. caliginosae (type strain, Ac9(T) = DSM 21895(T) = LMG 25312(T)) isolated from the nephridia of the earthworms Aporrectodea tuberculata and A. caliginosa, respectively.

Comparison of midgut bacterial diversity in tropical caterpillars (Lepidoptera: Saturniidae) fed on different diets

As primary consumers of foliage, caterpillars play essential roles in shaping the trophic structure of tropical forests. The caterpillar midgut is specialized in plant tissue processing; its pH is exceptionally alkaline and contains high concentrations of toxic compounds derived from the ingested plant material (secondary compounds or allelochemicals) and from the insect itself. The midgut, therefore, represents an extreme environment for microbial life. Isolates from different bacterial taxa have been recovered from caterpillar midguts, but little is known about the impact of these microorganisms on caterpillar biology. Our long-term goals are to identify midgut symbionts and to investigate their functions. As a first step, different diet formulations were evaluated for rearing two species of tropical saturniid caterpillars. Using the polymerase chain reaction (PCR) with primers hybridizing broadly to sequences from the bacterial domain, 16S rRNA gene libraries were constructed with midgut DNA extracted from caterpillars reared on different diets. Amplified rDNA restriction analysis indicated that bacterial sequences recovered from the midguts of caterpillars fed on foliage were more diverse than those from caterpillars fed on artificial diet. Sequences related to Methylobacterium sp., Bradyrhizobium sp., and Propionibacterium sp. were detected in all caterpillar libraries regardless of diet, but were not detected in a library constructed from the diet itself. Furthermore, libraries constructed with DNA recovered from surface-sterilized eggs indicated potential for vertical transmission of midgut symbionts. Taken together, these results suggest that microorganisms associated with the tropical caterpillar midgut may engage in symbiotic interactions with these ecologically important insects.

Beneficial effect of Verminephrobacter nephridial symbionts on the fitness of the earthworm Aporrectodea tuberculata

Almost all lumbricid earthworms (Oligochaeta: Lumbricidae) harbor species-specific Verminephrobacter (Betaproteobacteria) symbionts in their nephridia (excretory organs). The function of the symbiosis, and whether the symbionts have a beneficial effect on their earthworm host, is unknown; however, the symbionts have been hypothesized to enhance nitrogen retention in earthworms. The effect of Verminephrobacter on the life history traits of the earthworm Aporrectodea tuberculata (Eisen) was investigated by comparing the growth, development, and fecundity of worms with and without symbionts given high (cow dung)- and low (straw)-nutrient diets. There were no differences in worm growth or the number of cocoons produced by symbiotic and aposymbiotic worms. Worms with Verminephrobacter symbionts reached sexual maturity earlier and had higher cocoon hatching success than worms cured of their symbionts when grown on the low-nutrient diet. Thus, Verminephrobacter nephridial symbionts do have a beneficial effect on their earthworm host. Cocoons with and without symbionts did not significantly differ in total organic carbon, total nitrogen, or total hydrolyzable amino acid content, which strongly questions the hypothesized role of the symbionts in nitrogen recycling for the host.

Transmission of a bacterial consortium in Eisenia fetida egg capsules

The earthworm Eisenia fetida harbours Verminephrobacter eiseniae within their excretory nephridia. This symbiont is transferred from the parent into the egg capsules where the cells are acquired by the developing earthworm in a series of recruitment steps. Previous studies defined V. eiseniae as the most abundant cell type in the egg capsules, leaving approximately 30% of the bacteria unidentified and of unknown origin. The study presented here used terminal restriction fragment length polymorphism analysis together with cloning and sequencing of 16S rRNA genes to define the composition of the bacterial consortium in E. fetida egg capsules from early to late development. Newly formed capsules of E. fetida contained three bacterial types, a novel Microbacteriaceae member, a Flexibacteriaceae member and the previously described V. eiseniae. Fluorescent in situ hybridization (FISH) using specific and general rRNA probes demonstrated that the bacteria are abundant during early development, colonize the embryo and appear in the adult nephridia. As the capsules mature, Herbaspirillum spp. become abundant although they were not detected within the adult worm. These divergent taxa could serve distinct functions in both the adult earthworm and in the egg capsule to influence the competitive ability of earthworms within the soil community.

A complex journey: transmission of microbial symbionts

The perpetuation of symbioses through host generations relies on symbiont transmission. Horizontally transmitted symbionts are taken up from the environment anew by each host generation, and vertically transmitted symbionts are most often transferred through the female germ line. Mixed modes also exist. In this Review we describe the journey of symbionts from the initial contact to their final residence. We provide an overview of the molecular mechanisms that mediate symbiont attraction and accumulation, interpartner recognition and selection, as well as symbiont confrontation with the host immune system. We also discuss how the two main transmission modes shape the evolution of the symbiotic partners.

Common trends in mutualism revealed by model associations between invertebrates and bacteria

Mutually beneficial interactions between microorganisms and animals are a conserved and ubiquitous feature of biotic systems. In many instances animals, including humans, are dependent on their microbial associates for nutrition, defense, or development. To maintain these vital relationships, animals have evolved processes that ensure faithful transmission of specific microbial symbionts between generations. Elucidating mechanisms of transmission and symbiont specificity has been aided by the study of experimentally tractable invertebrate animals with diverse and highly evolved associations with microorganisms. Here, we review several invertebrate model systems that contribute to our current understanding of symbiont transmission, recognition, and specificity. Although the details of transmission and symbiont selection vary among associations, comparisons of diverse mutualistic associations are revealing a number of common themes, including restriction of symbiont diversity during transmission and glycan-lectin interactions during partner selection and recruitment.

Gut wall bacteria of earthworms: a natural selection process

Earthworms and microorganisms are interdependent and their interactions regulate the biogeochemistry of terrestrial soils. Investigating earthworm-microorganism interactions, we tested the hypothesis that differences in burrowing and feeding habits of anecic and endogeic earthworms are reflected by the existence of ecological group-specific gut wall bacterial communities. Bacterial community was detected using automated ribosomal intergenic spacer analysis of 16S and 23S genes and ribotype data was used to assess diversity and community composition. Using soil and earthworm samples collected from adjacent wheat-barley and grass-clover fields, we found that the anecic Lumbricus terrestris and L. friendi, the endogeic Aporrectodea caliginosa and A. longa (classically defined as anecic, but now known to possess endogeic characteristics) contain ecological group-specific gut wall-associated bacterial communities. The abundance of specific gut wall-associated bacteria (identified by sequence analysis of ribotype bands), including Proteobacteria, Firmicutes and an actinobacterium, was ecological group dependent. A microcosm study, conducted using A. caliginosa and L. terrestris and five different feeding regimes, indicated that food resource can cause shifts in gut wall-associated bacterial community, but the magnitude of these shifts did not obscure the delineation between ecological group specificity. Using A. caliginosa and A. longa samples collected in six different arable fields, we deduced that, within an ecological group, habitat was a more important determinant of gut wall-associated bacterial community composition than was host species. Hence, we conclude that the selection of bacteria associated with the gut wall of earthworms is a natural selection process and the strongest determinant of this process is in the order ecological group>habitat>species.

Diversity and host specificity of the Verminephrobacter-earthworm symbiosis

Symbiotic bacteria of the genus Verminephrobacter (Betaproteobacteria) were detected in the nephridia of 19 out of 23 investigated earthworm species (Oligochaeta: Lumbricidae) by 16S rRNA gene sequence analysis and fluorescence in situ hybridization (FISH). While all four Lumbricus species and three out of five Aporrectodea species were densely colonized by a mono-species culture of Verminephrobacter, other earthworm species contained mixed bacterial populations with varying proportions of Verminephrobacter; four species did not contain Verminephrobacter at all. The Verminephrobacter symbionts could be grouped into earthworm species-specific sequence clusters based on their 16S rRNA and RNA polymerase subunit B (rpoB) genes. Closely related host species harboured more closely related symbionts than did distantly related hosts. Co-diversification of the symbiotic partners could not be demonstrated unambiguously due to the poor resolution of the host phylogeny [based on histone H3 and cytochrome c oxidase subunit I (COI) gene sequence analyses]. However, there was a pattern of symbiont diversification within four groups of closely related hosts. The mean rate of symbiont 16S rRNA gene evolution was determined using a relaxed clock model, and the rate was calibrated with paleogeographical estimates of the time of origin of Lumbricid earthworms. The calibrated rates of symbiont 16S rRNA gene evolution are 0.012-0.026 substitutions per site per 50 million years and thus similar to rates reported from other symbiotic bacteria.

Stratified bacterial community in the bladder of the medicinal leech, Hirudo verbana

Most animals harbour symbiotic microorganisms inside their body, where intimate interactions occur between the partners. The medicinal leech, Hirudo verbana, possesses 17 pairs of excretory bladders that harbour a large number of intracellular and extracellular symbiotic bacteria. In this study, we characterized the bladder symbionts using molecular phylogenetic analyses, transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH). Restriction fragment length polymorphism (RFLP) and sequence analyses of 16S rRNA gene clone libraries suggested that six bacterial species co-colonize the leech bladders. Phylogenetic analyses revealed that these species belong to the alpha-Proteobacteria (Ochrobactrum symbiont), beta-Proteobacteria (Beta-1 and Beta-2 symbionts), delta-Proteobacteria (Bdellovibrio symbiont) and Bacteroidetes (Niabella and Sphingobacterium symbionts). Species-specific PCR detection and FISH confirmed the localization of the symbiotic bacteria in the bladders. The Ochrobactrum, Beta-1, Bdellovibrio and Sphingobacterium symbionts were consistently detected in 13 leeches from two populations, while infection rate of the other symbionts ranged between 20% and 100% in the two leech populations. Transmission electron microscopy observations of the bladders revealed epithelial cells harbouring a number of intracellular bacilli and an additional type of extracellular, rod-shaped bacteria in the luminal region. Fluorescence in situ hybridization with group-specific oligonucleotide probes revealed the spatial organization of the bacterial species in the bladder: the Ochrobactrum symbiont was located intracellularly inside epithelial cells; the Bacteroidetes were localized close to the epithelium in the lumen of the bladder; and the Bacteroidetes layer was covered with dense beta-proteobacterial cells. These results clearly demonstrate that a simple but organized microbial community exists in the bladder of the medicinal leech.

'Candidatus Lumbricincola', a novel lineage of uncultured Mollicutes from earthworms of family Lumbricidae

Molecular signatures of new, as yet uncultured mollicute-like organisms (MLOs) have been detected in total rRNA and DNA extracted from tissues, gut contents and casts of four species of the earthworm family Lumbricidae. The MLO 16S rRNA sequences exhibited low identity to those of known Mollicutes species and formed a monophyletic cluster distantly affiliated to the 'Candidatus Bacilloplasma' (84.9%) and almost equidistant to the other main phylogenetic group of Mollicutes (< 79.8%) and the classes Bacilli (< 79.5%) and Clostridia (< 76.1%). SSCP profiling and sequence analysis of bands and bacterial clones derived from the earthworms and substrata revealed high phylogenetic relatedness of MLOs in earthworms from different geographic locations (Russia and Germany), with no obvious host species specificity being observed. Fluorescence in situ hybridization (FISH) analysis with a nucleotide probe specific for the new MLO group localized them to the coelomic fluids of earthworms. A new taxonomic group within the Mollicutes, designated 'Candidatus Lumbricincola', is proposed to include these as yet uncultured organisms.

Implementation of artificial neural networks (ANNs) to analysis of inter-taxa communities of benthic microorganisms and macroinvertebrates in a polluted stream

This study was performed to gain an understanding of the structural and functional relationships between inter-taxa communities (macroinvertebrates as consumers, and microbes as decomposers or preys for the invertebrates) in a polluted stream using artificial neural networks techniques. Sediment samples, carrying microorganisms (eubacteria) and macroinvertebrates, were seasonally collected from similar habitats in streams with different levels of pollution. Microbial community taxa and densities were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA sequence analysis techniques. The identity and density of macroinvertebrates were concurrently determined. In general, differences were observed on grouping by self-organizing map (SOM) in polluted, clean and recovering sites based on the microbial densities, while the community patterns were partly dependent on the sampling period. A Spearman rank order correlation analysis revealed correlations of several eubacterial species with those of macroinvertebrates: a negative correlation was observed between Acidovorax sp. (from polluted sites) and Gammaridae (mostly from the clean site), while Herbaspirillum sp. and Janthinobacterium sp. appeared to have positive correlations with some macroinvertebrate species. The population dynamics of the tolerant texa, Tubificidae and Chironomidae, appeared to be related with changes in the densities of Acidovorax sp. This study revealed community relationships between macroinvertebrates and microorganisms, reflecting the connectivity between the two communities via the food chain. A further physio-ecological and symbiological study on the invertebrate-microorganism relationships will be required to understand the degradation and utilization of detritus in aquatic ecosystems as well as to elucidate the roles of the inter-taxa in the recovery of polluted aquatic environments.

As the Worm Turns: The Earthworm Gut as a Transient Habitat for Soil Microbial Biomes

The gut of the earthworm constitutes a mobile anoxic microzone to which the microorganisms of aerated soils are subjected. During gut passage, the in situ factors of the earthworm gut, which include anoxia and high concentrations of organic substrates, appear to greatly stimulate a subset of ingested soil microorganisms, including denitrifying and fermentative bacteria. The selective stimulation of ingested soil microbes by the unique microconditions of the earthworm gut (a) results in the in vivo emission of denitrification-derived dinitrogen (N(2)) and the greenhouse gas nitrous oxide (N(2)O) by the earthworm, and (b) might affect the fitness, culturability, and diversity of certain members of soil microbial biomes. These observations illustrate the impact that soil macrofauna might have on terrestrial nitrogen cycle processes via their transient hosting of ingested prokaryotes.

Enigmatic dual symbiosis in the excretory organ of Nautilus macromphalus (Cephalopoda: Nautiloidea)

Symbiosis is an important driving force in metazoan evolution and the study of ancient lineages can provide an insight into the influence of symbiotic associations on morphological and physiological adaptations. In the 'living fossil' Nautilus, bacterial associations are found in the highly specialized pericardial appendage. This organ is responsible for most of the excretory processes (ultrafiltration, reabsorption and secretion) and secretes an acidic ammonia-rich excretory fluid. In this study, we show that Nautilus macromphalus pericardial appendages harbour a high density of a beta-proteobacterium and a coccoid spirochaete using transmission electron microscopy, comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH). These two bacterial phylotypes are phylogenetically distant from any known bacteria, with ammonia-oxidizing bacteria as the closest relatives of the beta-proteobacterium (above or equal to 87.5% sequence similarity) and marine Spirochaeta species as the closest relatives of the spirochaete (above or equal to 89.8% sequence similarity), and appear to be specific to Nautilus. FISH analyses showed that the symbionts occur in the baso-medial region of the pericardial villi where ultrafiltration and reabsorption processes take place, suggesting a symbiotic contribution to the excretory metabolism.

Leeches and their microbiota: naturally simple symbiosis models

Strictly blood-feeding leeches and their limited microbiota provide natural and powerful model systems to examine symbiosis. Blood is devoid of essential nutrients and it is thought that symbiotic bacteria synthesize these for the host. In this review, three distinct leech-microbe associations are described: (i) the mycetome, which is the large symbiont-containing organ associated with the esophagus; (ii) the nephridia and bladders that form the excretory system; and (iii) the digestive tract, where two bacterial species dominate the microbiota. The current knowledge and features of leech biology that promote the investigation of interspecific interactions (host-microbe and microbe-microbe) and their evolution are highlighted.

Transmission of nephridial bacteria of the earthworm Eisenia fetida

The lumbricid earthworms (annelid family Lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. Comparative 16S rRNA gene sequencing of bacteria associated with the nephridia of several earthworm species has shown that each species of worm harbors a distinct bacterial species and that the bacteria from different species form a monophyletic cluster within the genus Acidovorax, suggesting that there is a specific association resulting from radiation from a common bacterial ancestor. Previous microscopy and culture studies revealed the presence of bacteria within the egg capsules and on the surface of embryos but did not demonstrate that the bacteria within the egg capsule were the same bacteria that colonized the nephridia. We present evidence, based on curing experiments, in situ hybridizations with Acidovorax-specific probes, and 16S rRNA gene sequence analysis, that the egg capsules contain high numbers of the bacterial symbiont and that juveniles are colonized during development within the egg capsule. Studies exposing aposymbiotic hatchlings to colonized adults and their bedding material suggested that juvenile earthworms do not readily acquire bacteria from the soil after hatching but must be colonized during development by bacteria deposited in the egg capsule. Whether this is due to the developmental stage of the host or the physiological state of the symbiont remains to be investigated.