Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris

Changes in arsenic mobility and speciation across a 2000-year-old paddy soil chronosequence

Rice accumulates arsenic (As) when cultivated under flooded conditions in paddy soils threatening rice yield or its safety for human consumption, depending on As speciation. During long-term paddy use, repeated redox cycles systematically alter soil biogeochemistry and microbiology. In the present study, incubation experiments from a 2000-year-old paddy soil chronosequence revealed that As mobilization and speciation also change with paddy soil age. Younger paddies (≤100 years) showed the highest total As mobilization, with speciation dominated by carcinogenic inorganic oxyarsenic species and highly mobile inorganic thioarsenates. Inorganic thioarsenates formed by a high availability of reduced sulfur (S) due to low concentrations of reducible iron (Fe) and soil organic carbon (SOC). Long-term paddy use (>100 years) resulted in higher microbial activity and SOC, increasing the share of phytotoxic methylated As. Methylated oxyarsenic species are precursors for cytotoxic methylated thioarsenates. Methylated thioarsenates formed in soils of all ages being limited either by the availability of methylated As in young soils or that of reduced-S in older ones. The present study shows that via a linkage of As to the biogeochemistry of Fe, S, and C, paddy soil age can influence the kind and the extent of threat that As poses for rice cultivation.

Dynamics of bacterial community in the foregut and hindgut of earthworms with the nutrition supplied by kitchen waste during vermicomposting

Earthworm gut microbiota is vital in degrading bio-waste during vermicomposting. However, microbial dynamics in earthworm gut during this process are unclear. Thus, the aim is to firstly report the bacterial dynamics in both foregut and hindgut of earthworms over a 28 days' timeframe of vermicomposting by Eisenia foetida with the nutrition supplied by kitchen waste. Results showed that except the changing of the bacterial diversity, composition and structure, dynamics of the foregut and hindgut bacteria also differed during vermicomposting which related to the changes of nutrient provision. Day 3 was a turning point. The abundant bacteria of the top 20 % genera nearly did not overlap between the foregut and hindgut. In the end of vermicomposting, a remarkable stable bacterial structure appeared in the hindgut compared to somewhat muddled one in the foregut. Understanding the dynamics of earthworm gut microbiota enables the improvements to regulate the efficiency of organic waste vermicomposting.

Variations in bacterial taxonomic profiles and potential functions in response to the gut transit of earthworms (Eisenia fetida) feeding on cow manure

Earthworms play an important role in the organic matter decomposition in terrestrial ecosystems. Earthworms interact directly with the microorganisms to affect the organic matter decomposition via gut transit, i.e., the digestion and assimilation of organic matter in the foregut and midgut and its excretion by the hindgut. However, how the microbial community ingested by earthworms respond to the transit processes in different gut segments of earthworms is not clear. We used composted cow manure to feed earthworms and sampled vermicompost and the contents of foregut, midgut and hindgut for bacterial 16S rRNA gene sequencing analysis. We observed that earthworm gut transit decreased the abundances of the dominant phyla Proteobacteria and Bacteroidetes but increased Actinobacteria, Chloroflexi and Acidobacteria. The alpha diversity of bacterial community in midgut was the lowest of the different gut segments, and the bacterial community structure of the foregut was significantly different from the midgut and hindgut. The enrichment analysis results revealed different selective stimulatory and inhibitory effects on the ingested bacterial community in the different gut segments, which extended to vermicompost. The FAPROTAX data indicated that C and N metabolic microbes were enriched in the earthworm gut. Microbes involved in fermentation and methanogenesis were enriched in the hindgut, and denitrification microbes were enriched in the foregut. The N metabolism microbes in vermicompost were significantly enriched after the stimulation of earthworm gut transit (P < 0.05), and the pathogenic microbes of animals and plants were inhibited. Combined with the results of subsequent correlation and biochemical analyses, earthworm gut transit significantly altered the structure and function of the bacterial community to accelerate the degradation and mineralization of organic matter and the enrichment of phosphorus and potassium. Our study suggests that the gut transit process of earthworms plays an important role in regulating organic matter dynamics in terrestrial ecosystems.

Ecological role of earthworm intestinal bacteria in terrestrial environments: A review

Increasing evidence demonstrated the critical role the earthworm gut played in sustaining earthworm's metabolism and transformation of nutrients and pollutants in the environment. Being rich in nutrients, the earthworm gut is favorable for the colonization of (facultative) anaerobic bacteria, which bridge the host earthworm gut with adjacent terrestrial environment. Therefore, the status quo of earthworm gut research was primarily reviewed in this work. It was found that most studies focused on the bacterial composition and diversity of the earthworm gut, and their potential application in nutrient element and pollutant transformation, such as nitrification, methanogens, heavy metal detoxification, etc. Yet limited information was available about the specific mechanism of intestinal bacteria in nutrient and pollutant transformation. Therefore, in this work we highlighted the current problems and concluded the future prospect of worm's intestinal bacteria research. On one hand, high throughput sequencing and bioinformatics tools are critical to break the bottleneck in the intestinal bacteria research via clarifying the molecular mechanism involved in the transformation processes described above. In addition, a global dataset concerning worm gut bacteria will be needed to provide comprehensive information about intestinal bacteria pool, and act as a communication platform to further encourage the progress of worm gut research.

Impact of water content and dietary organic carbon richness on gut bacteria in the earthworm Lumbricus terrestris

Many higher and lower animal gut ecosystems have complex resident microbial communities. In contrast, ingested soil is the primary source of the gut microbial diversity of earthworms, invertebrates of fundamental importance to the terrestrial biosphere. Earthworms also harbor a few endemic bacteria including Tenericutes-affiliated Candidatus Lumbricincola of unknown function. Gut microbes are subject to nutrient fluctuations due to dilution effects during gut passage, the nutrient richness of the anoxic gut, and dietary organic carbon, factors that could alter their activity/detection. This study's objective was to assess the potential impact of these factors on the occurrence and activity of ingested and endemic bacteria in gut content of Lumbricus terrestris. Fermentation product profiles of anoxic undiluted and diluted gut content treatments were similar, suggesting that experimental increase in water content and nutrient dilution had marginal impact on fermentation. However, 16S ribosomal Ribonucleic Acid (16S rRNA) sequence abundances indicated that stimulated bacterial taxa were not identical in undiluted and diluted treatments, with dominate potentially functionally redundant phylotypes being affiliated to the Firmicutes, Fusobacteria and Proteobacteria. Although the earthworm-associated Tenericutes were not stimulated in these treatments, the occurrence of three Tenericutes-affiliated phylotypes varied with the organic carbon richness of the earthworm diet, with two phylotypes being associated with high organic carbon richness. 16S rRNA sequence abundances indicated that other dominant gut taxa also varied with dietary organic carbon richness. These findings illustrate that functionally redundant ingested bacteria and earthworm-associated Tenericutes might be influenced by nutrient fluctuations in the gut and organic carbon richness of the earthworm diet.

Transovarial Transmission of Bacteriome-Associated Symbionts in the Cicada Pycna repanda (Hemiptera: Cicadidae)

Although transovarial transmission of bacteriome-associated symbionts in hemipteran insects is extremely important for maintaining intimate host-symbiont associations, our knowledge of cellular mechanisms underlying the transmission process is quite limited. We investigated bacterial communities of salivary glands, bacteriomes, and digestive and reproductive organs and clarified the transovarial transmission of bacteriome-associated symbionts of the mountain-habitat specialist Pycna repanda using integrated methods. The bacterial communities among different gut tissues and those of bacteriomes of males and females both show similarity, whereas differences are exhibited among bacterial communities in testes and ovaries. The primary symbionts "Candidatus Sulcia muelleri" (hereafter "Ca Sulcia") and "Candidatus Hodgkinia cicadicola" (hereafter "Ca Hodgkinia") were not only restricted to but also dominant in the bacteriomes and ovaries. "Ca Hodgkinia" cells in the bacteriomes of both sexes exhibited different colors by histological and electron microscopy. Also considering the results of a restriction fragment length polymorphism (RFLP)-based cloning approach, we hypothesize that "Ca Hodgkinia" may have split into cytologically different cellular lineages within this cicada species. Regarding the dominant secondary symbionts, Rickettsia was detected in the salivary glands, digestive organs, and testes, whereas Arsenophonus was detected in the bacteriomes and ovaries. Our results show that Arsenophonus can coexist with "Ca Sulcia" and "Ca Hodgkinia" within bacteriomes and can be transovarially transmitted with these obligate symbionts together from mother to offspring in cicadas, but it is not harbored in the cytoplasm of "Ca Sulcia." The change in the shape of "Ca Sulcia" and "Ca Hodgkinia" during the transovarial transmission process is hypothesized to be related to the limited space and novel microenvironment.IMPORTANCE Cicadas establish an intimate symbiosis with microorganisms to obtain essential nutrients that are extremely deficient in host plant sap. Previous studies on bacterial communities of cicadas mainly focused on a few widely distributed species, but knowledge about mountain-habitat species is quite poor. We initially revealed the physical distribution of the primary symbionts "Ca Sulcia" and "Ca Hodgkinia" and the dominant secondary symbionts Rickettsia and Arsenophonus in the mountain-habitat specialist Pycna repanda and then clarified the transovarial transmission process of bacteriome-associated symbionts in this species. Our observations suggest that "Ca Hodgkinia" may have split into cytologically distinct lineages within this cicada species, and related cicadas might have developed complex mechanisms for the vertical transmission of the bacteriome-associated symbionts. We also revealed that Arsenophonus can be transovarially transmitted in auchenorrhynchan insects when it is not harbored in the cytoplasm of other endosymbionts. Our results highlight transovarial transmission mechanisms of bacteriome-associated symbionts in sap-feeding insects.

Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management

Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.

Amino Acids and Ribose: Drivers of Protein and RNA Fermentation by Ingested Bacteria of a Primitive Gut Ecosystem

Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere.

Earthworms are among the most primitive animals and are of fundamental importance to the turnover of organic matter in the terrestrial biosphere. These invertebrates ingest materials that are colonized by microbes, some of which are subject to disruption by the crop/gizzard or other lytic events during gut passage. Protein and RNA are dominant polymers of disrupted microbial cells, and these biopolymers facilitate robust fermentations by surviving ingested bacteria. To further resolve these fermentations, amino acids and ribose (as fermentable constituents of protein and RNA, respectively) were evaluated as potential drivers of fermentation in gut content of the model earthworm Lumbricus terrestris (taxa were examined with 16S rRNA-based analyses). Of eight amino acids tested, glutamate, aspartate, and threonine were most stimulatory and yielded dissimilar fermentations facilitated by contrasting taxa (e.g., glutamate stimulated the Fusobacteriaceae and yielded H₂ and formate, whereas aspartate stimulated the Aeromonadaceae and yielded succinate and propionate). A marginal Stickland fermentation was associated with the Peptostreptococcaceae and Lachnospiraceae. Ribose fermentation yielded a complex product profile facilitated primarily by the Aeromonadaceae. The transient nature of succinate was linked to its decarboxylation to propionate and the Fusobacteriaceae, whereas the transient nature of formate was linked to formate-hydrogen lyase activity and the Peptostreptococcaceae. These findings reinforce the likelihood that (i) the animal host and hosted fermentative bacteria compete for the constituents of protein and RNA in the alimentary canal and (ii) diverse gut fermenters engaged in the fermentation of these constituents produce products that can be utilized by earthworms.

IMPORTANCE Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere.