Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens

We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general.

IMPORTANCE

Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.

Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated

BACKGROUND

With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts.

RESULTS

Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.).

CONCLUSIONS

Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.

Coal seam gas industry methane emissions in the Surat Basin, Australia: comparing airborne measurements with inventories

Coal seam gas (CSG) accounts for about one-quarter of natural gas production in Australia and rapidly increasing amounts globally. This is the first study worldwide using airborne measurement techniques to quantify methane (CH4) emissions from a producing CSG field: the Surat Basin, Queensland, Australia. Spatially resolved CH4 emissions were quantified from all major sources based on top-down (TD) and bottom-up (BU) approaches, the latter using Australia's UNFCCC reporting workflow. Based on our TD-validated BU inventory, CSG sources emit about 0.4% of the produced gas, comparable to onshore dry gas fields in the USA and The Netherlands, but substantially smaller than in other onshore regions, especially those where oil is co-produced (wet gas). The CSG CH4 emission per unit of gas production determined in this study is two to three times higher than existing inventories for the region. Our results indicate that the BU emission factors for feedlots and grazing cattle need review, possibly requiring an increase for Queensland's conditions. In some subregions, the BU estimate for gathering and boosting stations is potentially too high. The results from our iterative BU inventory process, which feeds into TD data, illustrate how global characterization of CH4 emissions could be improved by incorporating empirical TD verification surveys into national reporting. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 1)'.

CH4/CO2 Ratios and Carbon Isotope Enrichment Between Diet and Breath in Herbivorous Mammals

Breath and diet samples were collected from 29 taxa of animals at the Zurich and Basel Zoos to characterize the carbon isotope enrichment between breath and diet. Diet samples were measured for δ13C and breath samples for CH4/CO2 ratios and for the respired component of δ13C using the Keeling plot approach. Different digestive physiologies included coprophagous and non-coprophagous hindgut fermenters, and non-ruminant and ruminant foregut fermenters. Isotope enrichments from diet to breath were 0.8 ± 0.9‰, 3.5 ± 0.8‰, 2.3 ± 0.4‰, and 4.1 ± 1.0‰, respectively. CH4/CO2 ratios were strongly correlated with isotope enrichments for both hindgut and foregut digestive strategies, although CH4 production was not the sole reason for isotope enrichment. Average CH4/CO2 ratios per taxon ranged over several orders of magnitude from 10–5 to 10–1. The isotope enrichment values for diet-breath can be used to further estimate the isotope enrichment from diet-enamel because Passey et al. (2005b) found a nearly constant isotope enrichment for breath-enamel for diverse mammalian taxa. The understanding of isotope enrichment factors from diet to breath and diet to enamel will have important applications in the field of animal physiology, and possibly also for wildlife ecology and paleontology.

Review: Comparative methane production in mammalian herbivores

Methane (CH4) production is a ubiquitous, apparently unavoidable side effect of fermentative fibre digestion by symbiotic microbiota in mammalian herbivores. Here, a data compilation is presented of in vivo CH4 measurements in individuals of 37 mammalian herbivore species fed forage-only diets, from the literature and from hitherto unpublished measurements. In contrast to previous claims, absolute CH4 emissions scaled linearly to DM intake, and CH4 yields (per DM or gross energy intake) did not vary significantly with body mass. CH4 physiology hence cannot be construed to represent an intrinsic ruminant or herbivore body size limitation. The dataset does not support traditional dichotomies of CH4 emission intensity between ruminants and nonruminants, or between foregut and hindgut fermenters. Several rodent hindgut fermenters and nonruminant foregut fermenters emit CH4 of a magnitude as high as ruminants of similar size, intake level, digesta retention or gut capacity. By contrast, equids, macropods (kangaroos) and rabbits produce few CH4 and have low CH4 : CO2 ratios for their size, intake level, digesta retention or gut capacity, ruling out these factors as explanation for interspecific variation. These findings lead to the conclusion that still unidentified host-specific factors other than digesta retention characteristics, or the presence of rumination or a foregut, influence CH4 production. Measurements of CH4 yield per digested fibre indicate that the amount of CH4 produced during fibre digestion varies not only across but also within species, possibly pointing towards variation in microbiota functionality. Recent findings on the genetic control of microbiome composition, including methanogens, raise the question about the benefits methanogens provide for many (but apparently not to the same extent for all) species, which possibly prevented the evolution of the hosting of low-methanogenic microbiota across mammals.

Methane emissions of geese (Anser anser) and turkeys (Meleagris gallopavo) fed pelleted lucerne

In contrast to mammalian herbivores, birds are generally perceived to produce little methane (CH₄) during digestion, and accounting for poultry in greenhouse gas inventories is considered unnecessary. We measured CH₄ emissions in six domestic geese (Anser anser, 5.0 ± 0.9 kg) and six domestic turkeys (Meleagris gallopavo, 6.3 ± 0.6 kg) kept on a diet of lucerne pellets only, using open-circuit chamber respirometry. Measurements of oxygen consumption were similar to previously published values in these species. Absolute CH₄ emissions per day were lower in geese (0.58 ± 0.10 L) than in turkeys (1.48 ± 0.16 L) and represented 0.4 ± 0.2 and 0.6 ± 0.1% of gross energy intake, respectively. These results confirm previous findings on the presence of methanogenes in the digestive tract of poultry species, and in vitro measurements performed on poultry caecal contents. In relation to mammalian herbivores in terms of absolute CH₄ emissions, CH₄ yield per dry matter or gross energy intake, or the CH₄:CO₂ ratio, the lucerne-fed geese and turkeys had comparatively low values. The emission of CH₄ in spite of the very short digesta retention times and low fibre digestibility, as measured in the same animals, gives rise to the hypothesis that that in some birds, caecal fermentation and the associated CH₄ production may be related to the microbial digestion of uric acid. The hypothesis that CH₄ emissions in poultry may depend not only on dietary fibre but also on dietary digestible protein (that is excreted as uric acid in urine and retrogradely transported from the cloaca into the caeca) remains to be tested.

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus)

The quantification and community of bacteria in the gastrointestinal (GI) tract (stomach, jejunum, ileum, cecum, colon and rectum) of red kangaroos (Macropus rufus) were examined by using real-time PCR and paired-end Illumina sequencing. The quantification of bacteria showed that the number of bacteria in jejunum and rectum was significantly lower than that in colon and cecum (P < 0.05). A total of 1,872,590 sequences was remained after quality-filtering and 50,948 OTUs were identified at the 97 % similarity level. The dominant phyla in the GI tract of red kangaroos were identified as Actinobacteria, Bacteroidetes and Firmicutes. At the level of genus, the samples from different parts of GI tract clustered into three groups: stomach, small intestine (jejunum and ileum) and large intestine (cecum and rectum). Prevotella (29.81 %) was the most dominant genus in the stomach and significantly (P < 0.05) higher than that in other parts of GI tract. In the small intestine, Bifidobacterium (33.04, 12.14 %) and Streptococcus (22.90, 19.16 %) were dominant genera. Unclassified Ruminococcaceae was the most dominant family in large intestine and the total relative abundance of unclassified bacteria was above 50 %. In identified genera, Dorea was the most important variable to discriminate large intestine and it was significantly higher in cecum than in stomach, small intestine and colon (P < 0.05). Bifidobacterium (21.89 %) was the only dominant genus in colon. Future work on culture in vitro and genome sequencing of those unidentified bacteria might give us insight into the function of these microorganisms in the GI tract. In addition, the comparison of the bacterial community in the foregut of kangaroos and other herbivores and the rumen might give us insight into the mechanism of fiber degradation and help us exploit approaches to improve the feed efficiency and subsequently, reduce the methane emission from herbivores.