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 (N₂) and the greenhouse gas nitrous oxide (N₂O) 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.

Earthworms emit nitrous oxide (N₂O) via the activity of bacteria in their gut. Four N₂O-producing facultative aerobes, ED1^T, ED5^T, MH21^T and MH72, were isolated from the gut of the earthworm Aporrectodea caliginosa. The isolates produced N₂O under conditions that simulated the microenvironment of the earthworm gut. ED1^T and ED5^T were Gram-negative, motile rods that carried out complete denitrification (i.e. the reduction of nitrate to N₂) and contained membranous c-type cytochromes. ED1^T grew optimally at 30 °C and pH 7. ED1^T oxidized organic acids and reduced (per)chlorate, sulfate, nitrate and nitrite. The closest phylogenetic relative of ED1^T was Dechloromonas agitata. ED5^T grew optimally at 25 °C and pH 7. ED5^T grew mainly on sugars, and nitrate and nitrite were used as alternative electron acceptors. The closest phylogenetic relatives of ED5^T were Flavobacterium johnsoniae and Flavobacterium flevense. MH21^T and MH72 were motile, spore-forming, rod-shaped bacteria with a three-layered cell wall. Sugars supported the growth of MH21^T and MH72. Cells of MH21^T grew in chains, were linked by connecting filaments and contained membranous b-type cytochromes. MH21^T grew optimally at 30–35 °C and pH 7·7, grew by fermentation and reduced low amounts of nitrite to N₂O. The closest phylogenetic relatives of MH21^T were Paenibacillus borealis and Paenibacillus chibensis. Based on morphological, physiological and phylogenetic characteristics, ED1^T (=DSM 15892^T=ATCC BAA-841^T), ED5^T (=DSM 15936^T=ATCC BAA-842^T) and MH21^T (=DSM 15890^T=ATCC BAA-844^T) are proposed as type strains of the novel species Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov. and Paenibacillus anaericanus sp. nov., respectively. MH72 is considered a new strain of Paenibacillus terrae.

The emission of methane (1.3 mmol of CH ₄ m ⁻² day ⁻¹ ), precursors of methanogenesis, and the methanogenic microorganisms of acidic bog peat (pH 4.4) from a moderately reduced forest site were investigated by in situ measurements, microcosm incubations, and cultivation methods, respectively. Bog peat produced CH ₄ (0.4 to 1.7 μmol g [dry wt] of soil ⁻¹ day ⁻¹ ) under anoxic conditions. At in situ pH, supplemental H ₂ -CO ₂ , ethanol, and 1-propanol all increased CH ₄ production rates while formate, acetate, propionate, and butyrate inhibited the production of CH ₄ ; methanol had no effect. H ₂ -dependent acetogenesis occurred in H ₂ -CO ₂ -supplemented bog peat only after extended incubation periods. Nonsupplemented bog peat initially produced small amounts of H ₂ that were subsequently consumed. The accumulation of H ₂ was stimulated by ethanol and 1-propanol or by inhibiting methanogenesis with bromoethanesulfonate, and the consumption of ethanol was inhibited by large amounts of H ₂ ; these results collectively indicated that ethanol- or 1-propanol-utilizing bacteria were trophically associated with H ₂ -utilizing methanogens. A total of 10 ⁹ anaerobes and 10 ⁷ hydrogenotrophic methanogens per g (dry weight) of bog peat were enumerated by cultivation techniques. A stable methanogenic enrichment was obtained with an acidic, H ₂ -CO ₂ -supplemented, fatty acid-enriched defined medium. CH ₄ production rates by the enrichment were similar at pH 4.5 and 6.5, and acetate inhibited methanogenesis at pH 4.5 but not at pH 6.5. A total of 27 different archaeal 16S rRNA gene sequences indicative of Methanobacteriaceae , Methanomicrobiales , and Methanosarcinaceae were retrieved from the highest CH ₄ -positive serial dilutions of bog peat and methanogenic enrichments. A total of 10 bacterial 16S rRNA gene sequences were also retrieved from the same dilutions and enrichments and were indicative of bacteria that might be responsible for the production of H ₂ that could be used by hydrogenotrophic methanogens. These results indicated that in this acidic bog peat, (i) H ₂ is an important substrate for acid-tolerant methanogens, (ii) interspecies hydrogen transfer is involved in the degradation of organic carbon, (iii) the accumulation of protonated volatile fatty acids inhibits methanogenesis, and (iv) methanogenesis might be due to the activities of methanogens that are phylogenetic members of the Methanobacteriaceae , Methanomicrobiales , and Methanosarcinaceae .

Microplastic (MP) is a pervasive pollutant in nature that is colonised by diverse groups of microbes, including potentially pathogenic species. Fungi have been largely neglected in this context, despite their affinity for plastics and their impact as pathogens. To unravel the role of MP as a carrier of fungal pathogens in terrestrial ecosystems and the immediate human environment, epiplastic mycobiomes from municipal plastic waste from Kenya were deciphered using ITS metabarcoding as well as a comprehensive meta-analysis, and visualised via scanning electron as well as confocal laser scanning microscopy. Metagenomic and microscopic findings provided complementary evidence that the terrestrial plastisphere is a suitable ecological niche for a variety of fungal organisms, including important animal and plant pathogens, which formed the plastisphere core mycobiome. We show that MPs serve as selective artificial microhabitats that not only attract distinct fungal communities, but also accumulate certain opportunistic human pathogens, such as cryptococcal and Phoma-like species. Therefore, MP must be regarded a persistent reservoir and potential vector for fungal pathogens in soil environments. Given the increasing amount of plastic waste in terrestrial ecosystems worldwide, this interrelation may have severe consequences for the trans-kingdom and multi-organismal epidemiology of fungal infections on a global scale.

The in vivo production of nitrous oxide (N₂O) by earthworms is due to their gut microbiota, and it is hypothesized that the microenvironment of the gut activates ingested N₂O-producing soil bacteria. In situ measurement of N₂O and O₂with microsensors demonstrated that the earthworm gut is anoxic and the site of N₂O production. The gut had a pH of 6.9 and an average water content of approximately 50%. The water content within the gut decreased from the anterior end to the posterior end. In contrast, the concentration of N₂O increased from the anterior end to the mid-gut region and then decreased along the posterior part of the gut. Compared to the soil in which worms lived and fed, the gut of the earthworm was highly enriched in total carbon, organic carbon, and total nitrogen and had a C/N ratio of 7 (compared to a C/N ratio of 12 in soil). The aqueous phase of gut contents contained up to 80 mM glucose and numerous compounds that were indicative of anaerobic metabolism, including up to 9 mM formate, 8 mM acetate, 3 mM lactate, and 2 mM succinate. Compared to the soil contents, nitrite and ammonium were enriched in the gut up to 10- and 100-fold, respectively. The production of N₂O by soil was induced when the gut environment was simulated in anoxic microcosms for 24 h (the approximate time for passage of soil through the earthworm). Anoxia, high osmolarity, nitrite, and nitrate were the dominant factors that stimulated the production of N₂O. Supplemental organic carbon had a very minimal stimulatory effect on the production of N₂O, and addition of buffer or ammonium had essentially no effect on the initial N₂O production rates. However, a combination of supplements yielded rates greater than that obtained mathematically for single supplements, suggesting that the maximum rates observed were due to synergistic effects of supplements. Collectively, these results indicate that the special microenvironment of the earthworm gut is ideally suited for N₂O-producing bacteria and support the hypothesis that the in situ conditions of the earthworm gut activate ingested N₂O-producing soil bacteria during gut passage.