Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets

Composition of the rumen archaeal community of growing camels fed different concentrate levels

Understanding the rumen fermentation and methanogenic community in camels fed intensively is critical for optimizing rumen fermentation, improving feed efficiency, and lowering methane emissions. Using Illumina MiSeq sequencing, quantitative real-time PCR, and high-performance liquid chromatography, this study evaluates the influence of different concentrate supplement levels in the diet on rumen fermentation as well as the diversity and structure of the rumen methanogenic community for growing dromedary camels. Twelve growing camels were divided into three groups and given three levels of concentrate supplement, 0.7% (C1), 1% (C2), and 1.3% (C3) based on their body weight. All animals were fed alfalfa hay ad libitum. The levels of total volatile fatty acid, rumen ammonia, and methanogen copy number were unaffected by the supplementation level. Increasing the concentrate supplement level increased the proportion of propionic acid while decreasing the proportion of acetic acid. Increasing the level of concentrate in the diet had no effect on alpha diversity metrics or beta diversity of rumen methanogens. Methanobrevibacter and Methanosphaera predominated the methanogenic community and were declined as concentrate supplement level increased. This study sheds new light on the effect of concentrate supplement level in growing camels' diet on rumen fermentation and methanogenic community, which could help in the development of a strategy that aimed to reduce methane emissions and enhance feed efficiency.

The archaeal and bacterial community structure in composted cow manures is defined by the original populations: a shotgun metagenomic approach

Introduction

Organic wastes are composted to increase their plant nutritional value, but little is known about how this might alter the bacterial and archaeal community structure and their genes.

Methods

Cow manure was collected from three local small-scale farmers and composted under controlled conditions, while the bacterial and archaeal communities were determined using shotgun metagenomics at the onset and after 74 days of composting.

Results

The bacterial, archaeal, methanogen, methanotrophs, methylotroph, and nitrifying community structures and their genes were affected by composting for 74 days, but the original composition of these communities determined the changes. Most of these archaeal and bacterial groups showed considerable variation after composting and between the cow manures. However, the differences in the relative abundance of their genes were much smaller compared to those of the archaeal or bacterial groups.

Discussion

It was found that composting of different cow manures did not result in similar bacterial or archaeal communities, and the changes that were found after 74 days were defined by the original populations. However, more research is necessary to determine if other composting conditions will give the same results.

Inoculum microbial mass is negatively related to microbial yield and positively to methane yield in vitro

Ruminal microbes catabolise feed carbohydrates mainly into SCFA, methane (CH4), and carbon dioxide (CO2), with predictable relationships between fermentation end products and net microbial increase. We used a closed in vitro batch culture system, incubating grass and maize silages, and measured total gas production at 8 and 24 h, as well as the truly degraded substrate, the net production of SCFA, CH4, and microbial biomass at 24 h, and investigated the impact of silage type and inoculum microbial mass on fermentation direction. Net microbial yield was negatively correlated with total gas at 8 h (P < 0•001), but not at 24 h (P = 0•052), and negatively correlated with CH4 production (P < 0•001). Higher initial inoculum microbial mass was related to a lower net microbial yield (P < 0•001) but a higher CH4 production (P < 0•001). A significant difference between grass silage and maize silage was detected within the context of these relationships (P < 0•050). The metabolic hydrogen (2H) recovery was 102.8 ± 12.3 % for grass silages and 118.8 ± 13.3% for maize silages. Overall, grass silages favoured more substrate conversion to microbial biomass and less to fermentation end products than maize silage. Lower inoculum microbial mass facilitated more microbial growth and, because of the 2H sink by microbial synthesis, decreased CH4 production.

Effect of carbohydrate type in silages and concentrates on feed intake, enteric methane and milk yield from dairy cows

Dietary carbohydrate manipulation can be used to reduce enteric CH4 emission, but there is a lack of studies on the interaction of different types of carbohydrates that can affect feed intake and ruminal fermentation. Understanding this interaction is necessary to make the most out of CH4 mitigation feeding strategies using different dietary carbohydrates. The aim of this study was to test the effect on enteric CH4 emission, feed intake and milk production response when cows were fed either grass-clover (GCS) or corn silage (CS) as the sole forage source (55% of dry matter, DM), in combination with either barley (BAR) or dried beet pulp (DBP) as a concentrate (21.5% of DM). Twenty-four (half first and half second parity) cows were used in a crossover design with 2 periods of 21 d each, receiving 2 of 4 diets obtained from a 2 × 2 factorial arrangement of the experimental diet. Feed intake, CH4 emission metrics and milk production were recorded at the end of the experimental periods. The diets had NDF concentrations between 258 and 340 g/kg of DM, and starch concentrations between 340 and 7.45 g/kg of DM (CS-BAR and GCS-DBP, respectively). The effects of silage and concentrate on dry matter intake (DMI) were additive, with the highest feed intake in cows fed COR-BAR, followed by cows fed COR-DBP, GCS-BAR, and GCS-DBP (21.2, 19.9, 19.1, and 18.3 kg/d). Energy corrected milk (ECM) yield was not affected by silage source in first parity cows, but it was higher for cows fed CS than cows fed GCS in second parity. The effects of silage and concentrate on CH4 production (g/d), yield (g/kg of DMI) and intensity (g/kg of ECM) were not additive as cows fed GCS had similar responses regardless of the concentrate used, but cows fed CS had lower CH4 production, yield and intensity, when fed BAR instead of DBP. The lower CH4 production, yield and intensity in cows fed CS-BAR compared with other diets could be partially explained by the nonlinear relationship between ruminal VFA and carbohydrates (NDF and starch) concentration reported in literature, however, we observed a linear relationship between acetate:propionate ratio and CH4 yield, suggesting possible other effects. The effects of silage and concentrate on the ruminal VFA were additive in first parity cows, but not in second parity cows. The interaction between dietary CHO type and parity might indicate an effect of feed intake or the energy balance of the cow. Feeding cows silage and concentrate both rich in starch can result in the lowest enteric CH4 emission.

Tailored Nanoparticles With the Potential to Reduce Ruminant Methane Emissions

Agricultural methane produced by archaea in the forestomach of ruminants is a key contributor to rising levels of greenhouse gases leading to climate change. Functionalized biological polyhydroxybutyrate (PHB) nanoparticles offer a new concept for the reduction of enteric methane emissions by inhibiting rumen methanogens. Nanoparticles were functionalized in vivo with an archaeal virus lytic enzyme, PeiR, active against a range of rumen Methanobrevibacter species. The impact of functionalized nanoparticles against rumen methanogens was demonstrated in pure cultures, in rumen batch and continuous flow rumen models yielding methane reduction of up to 15% over 11 days in the most complex system. We further present evidence of biological nanoparticle fermentation in a rumen environment. Elevated levels of short-chain fatty acids essential to ruminant nutrition were recorded, giving rise to a promising new strategy combining methane mitigation with a possible increase in animal productivity.

Diets varying in ratio of sweet sorghum silage to corn silage for lactating dairy cows: Feed intake, milk production, blood biochemistry, ruminal fermentation, and ruminal microbial community

The objective of this study was to investigate the effects of partial substitution of corn silage (CS) with sweet sorghum silage (SS) in the diets of lactating dairy cows on dry matter (DM) intake, milk yield and composition, blood biochemistry, and ruminal fermentation and microbial community. Thirty mid-lactation Holstein dairy cows [mean ± standard deviation; 639 ± 42.0 kg of body weight; 112 ± 24.0 d in milk (DIM)] were assigned to 3 groups (n = 10/treatment) by considering parity, milk yield, and DIM. The cows were fed ad libitum total mixed rations containing 55% forage and 45% concentrate, with only the proportion of CS and SS varying in 3 treatments (DM basis): SS0 (0% substitution of CS), 40% CS and 0% SS; SS25 (25% substitution of CS)_, 30% CS and 10% SS; and SS50 (50% substitution of CS)_, 20% CS and 20% SS. Dry matter intake and milk protein concentration tended to linearly decrease with increasing proportion of SS in the diet. Yields of milk (mean ± standard deviation, 30.9 ± 1.12 kg/d), 4% fat-corrected milk (30.0 ± 0.81 kg/d), energy-corrected milk, milk protein, lactose, and total solids, concentrations of milk fat, lactose, somatic cell counts, and milk efficiency did not differ among diets. The concentrations in blood of urea nitrogen, phosphorus, aspartate aminotransferase, and malondialdehyde linearly increased with increasing SS proportion. Blood IgA decreased with increasing SS substitution rate, but blood IgG and IgM were not different among diets. Ruminal pH did not differ among diets, whereas ruminal NH₃-N concentration quadratically changed such that it was greater for SS50 than for SS0 and SS25. Molar proportions of propionate and acetate to propionate ratio were less for SS25 than for SS0. Although the diversity and general ruminal microbial community structure were not altered by partially replacing CS with SS, the relative abundances of predominant bacteria were affected by diets at the phylum and genus levels. Firmicutes and Bacteroidetes were dominant phyla in the ruminal bacterial community for all diets, and their relative abundance linearly decreased and increased, respectively, with increasing SS substitution rate. Prevotella_1 and Ruminococcaceae_NK4A214_group were detected as the most and the second most abundant genera, with their relative abundance linearly increased and decreased, respectively, with increasing SS substitution rate. The relative abundance of Fibrobacter linearly increased with increasing dietary SS proportion, with greater abundance observed for SS25 and SS50 than for SS0. These results suggest that substitution of CS with SS altered the relative abundances of some predominant bacteria; however, these changes had little effect on ruminal fermentation and milk yield. Under the current experimental conditions, substituting up to 50% of CS with SS had no negative effects on milk yield, indicating that SS can partially replace CS in the diets of high-producing lactating dairy cows without adding extra grain, when diets are fed for a short time. As the effects of substituting CS with SS depend upon the chemical composition and digestibility of these silages and the nutrient requirements of the cows, additional grain may be required in some cases to compensate for the lower starch content of SS.

Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?

The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.