The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition

Anaerobic fungi contain abundant, diverse, and transcriptionally active Long Terminal Repeat retrotransposons

Long Terminal Repeat (LTR) retrotransposons are a class of repetitive elements that are widespread in the genomes of plants and many fungi. LTR retrotransposons have been associated with rapidly evolving gene clusters in plants and virulence factor transfer in fungal-plant parasite-host interactions. We report here the abundance and transcriptional activity of LTR retrotransposons across several species of the early-branching Neocallimastigomycota, otherwise known as the anaerobic gut fungi (AGF). The ubiquity of LTR retrotransposons in these genomes suggests key evolutionary roles in these rumen-dwelling biomass degraders, whose genomes also contain many enzymes that are horizontally transferred from other rumen-dwelling prokaryotes. Up to 10% of anaerobic fungal genomes consist of LTR retrotransposons, and the mapping of sequences from LTR retrotransposons to transcriptomes shows that the majority of clusters are transcribed, with some exhibiting expression greater than 104 reads per kilobase million mapped reads (rpkm). Many LTR retrotransposons are strongly differentially expressed upon heat stress during fungal cultivation, with several exhibiting a nearly three-log10 fold increase in expression, whereas growth substrate variation modulated transcription to a lesser extent. We show that some LTR retrotransposons contain carbohydrate-active enzymes (CAZymes), and the expansion of CAZymes within genomes and among anaerobic fungal species may be linked to retrotransposon activity. We further discuss how these widespread sequences may be a source of promoters and other parts towards the bioengineering of anaerobic fungi.

Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.

Response of rumen microorganisms to pH during anaerobic hydrolysis and acidogenesis of lignocellulose biomass

Rumen microorganisms can efficiently degrade lignocellulosic wastes to produce volatile fatty acids (VFAs). pH is a key factor in controlling the type and yield of VFAs by affecting the microorganisms involved in rumen fermentation. However, the effects of different pH on rumen microbial diversity, communities, and mechanisms are unclear. In this study, the hydrolysis and acidogenesis of corn straw and diversity, communities, and mechanisms of rumen microorganisms were explored at different initial pHs. Results showed that the highest hemicellulose, cellulose, and lignin degradation efficiency of corn straw was 55.2 %, 38.3 %, and 7.01 %, respectively, and VFA concentration was 10.2 g/L at pH 7.0. Low pH decreased the bacterial diversity and increased the fungal diversity. Rumen bacteria and fungi had different responses to initial pHs, and the community structure of bacteria and fungi had obviously differences at the genus level. The core genera Succiniclasticum, Treponema, and Neocallimastix relative abundance at initial pH 7.0 samples were significantly higher than that at lower initial pHs, reaching 6.01 %, 1.61 %, and 5.35 %, respectively. The bacterial network was more complex than that of fungi. pH, acetic acid, and propionic acid were the main factors influencing the bacterial and fungal community structure. Low pH inhibited the expression of functional genes related to hydrolysis and acidogenesis, explaining the lower hydrolysis and acidogenesis efficiency. These findings will provide a better understanding for rumen fermentation to produce VFAs.

Temporal progression of anaerobic fungal communities in dairy calves from birth to maturity

Establishment of microbial communities in neonatal calves is vital for their growth and overall health. While this process has received considerable attention for bacteria, our knowledge on temporal progression of anaerobic gut fungi (AGF) in calves is lacking. Here, we examined AGF communities in faecal samples from six dairy cattle collected at 24 different time points during the pre-weaning (days 1-48), weaning (days 48-60), and post-weaning (days 60-360) phases. Quantitative polymerase chain reaction indicated that AGF colonisation occurs within 24 h after birth, with loads slowly increasing during pre-weaning and weaning, then drastically increasing post-weaning. Culture-independent amplicon surveys identified higher alpha diversity during pre-weaning/weaning, compared to post-weaning. AGF community structure underwent a drastic shift post-weaning, from a community enriched in genera commonly encountered in hindgut fermenters to one enriched in genera commonly encountered in adult ruminants. Comparison of AGF community between calves day 1 post-birth and their mothers suggest a major role for maternal transmission, with additional input from cohabitating subjects. This distinct pattern of AGF progression could best be understood in-light of their narrower niche preferences, metabolic specialisation, and physiological optima compared to bacteria, hence eliciting a unique response to changes in feeding pattern and associated structural GIT development during maturation.

Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment

Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.

Quantitative microbiome profiling reveals the developmental trajectory of the chicken gut microbiota and its connection to host metabolism

Revealing the assembly and succession of the chicken gut microbiota is critical for a better understanding of its role in chicken physiology and metabolism. However, few studies have examined dynamic changes of absolute chicken gut microbes using the quantitative microbiome profiling (QMP) method. Here, we revealed the developmental trajectory of the broiler chicken gut bacteriome and mycobiome by combining high-throughput sequencing with a microbial load quantification assay. We showed that chicken gut microbiota abundance and diversity reached a plateau at 7 days posthatch (DPH), forming segment-specific community types after 1 DPH. The bacteriome was more impacted by deterministic processes, and the mycobiome was more affected by stochastic processes. We also observed stage-specific microbes in different gut segments, and three microbial occurrence patterns including "colonization," "disappearance," and "core" were defined. The microbial co-occurrence networks were very different among gut segments, with more positive associations than negative associations. Furthermore, we provided links between the absolute changes in chicken gut microbiota and their serum metabolite variations. Time-course untargeted metabolomics revealed six metabolite clusters with different changing patterns of abundance. The foregut microbiota had more connections with chicken serum metabolites, and the gut microbes were closely related to chicken lipid and amino acid metabolism. The present study provided a full landscape of chicken gut microbiota development in a quantitative manner, and the associations between gut microbes and chicken serum metabolites further highlight the impact of gut microbiota in chicken growth and development.

Suitability of anaerobic fungi culture supernatant or mixed ruminal fluid as novel silage additives

Abstract

This study investigated silage quality characteristics and ruminal fiber degradability of grass and straw ensiled with either anaerobic fungi (AF) supernatant with active fungal enzymes or mixed ruminal fluid as novel silage additives. Compared to control silages, AF supernatant improved the quality of grass and straw silages as evidenced by decreased pH, acetic acid concentration, and dry matter losses. Likewise, mixed ruminal fluid enhanced lactic acid fermentation, which further resulted in lower pH of the treated grass silage. The ruminal fiber degradability was determined using in situ incubations and, compared to controls, the cellulose degradability was higher for grass silage with AF supernatant, whereas ruminal degradability of straw silage was reduced by this treatment. In contrast, mixed ruminal fluid did not influence fiber degradability of silages in the rumen. Concluding, both novel additives improved silage quality, whereas only AF supernatant enhanced ruminal fiber degradability of grass silage and therefore may represent an approach for improving forage utilization by ruminants.

Key points

• Enzymes of anaerobic fungi supernatant improve quality of grass and straw silages.

• Mixed ruminal fluid enhances lactic acid fermentation when ensiling grass and straw.

• Enzymes of anaerobic fungi supernatant increase ruminal grass silage degradability.

Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara).

Rumen Metaproteomics Highlight the Unique Contributions of Microbe-Derived Extracellular and Intracellular Proteins for In Vitro Ruminal Fermentation

Rumen microorganisms can be used in in vitro anaerobic fermentation to encourage the sustainable exploitation of agricultural wastes. However, the understanding of active microbiota under in vitro ruminal fermentation conditions is still insufficient. To investigate how rumen microbes actively participate in the fermentation process in vitro, we resolved the metaproteome generated from ruminal fermentation broth after seven days of in vitro incubation. Herein, the sample-specific database for metaproteomic analysis was constructed according to the metagenomic data of in vitro ruminal fermentation. Based on the sample-specific database, we found in the metaproteome that Bacteroidetes and Firmicutes_A were the most active in protein expression, and over 50% of these proteins were assigned to gene categories involved in energy conversion and basic structures. On the other hand, a variety of bacteria-derived extracellular proteins, which contained carbohydrate-active enzyme domains, were found in the extracellular proteome of fermentation broth. Additionally, the bacterial intracellular/surface moonlighting proteins (ISMPs) and proteins of outer membrane vesicles were detected in the extracellular proteome, and these ISMPs were involved in maintaining microbial population size through potential adherence to substrates. The metaproteomic characterizations of microbial intracellular/extracellular proteins provide new insights into the ability of the rumen microbiome to maintain in vitro ruminal fermentation.

Effects of Bovine Pichia kudriavzevii T7, Candida glabrata B14, and Lactobacillus plantarum Y9 on Milk Production, Quality and Digestive Tract Microbiome in Dairy Cows

Microbial administration has been used successfully to improve host health. However, the positive effects of endogenous microbials are still underexplored. This study investigated the effects of bovine Lactic acid bacteria and yeast on the milk production, quality and digestive tract microbiome of dairy cows. Lactobacillus plantarum Y9, Pichia kudriavzevii T7 and Candida glabrata B14 isolated from high-yielding dairy cows were selected to feed low-yielding Holstein cows. Pichia kudriavzevii T7 could significantly increase milk yield, meanwhile, Pichia kudriavzevii T7 and Candida glabrata B14 could obviously reduce the number of somatic cell counts (SCC). However, slight differences were found in milk fat, protein, lactose and SNF (solids not fat) percentage. High throughput sequencing showed that the dominant bacteria were Prevotella and Ruminococcaceae in rumen and feces, respectively, and the dominant fungi were Penicillium, Aspergillus and Trichoderma in both samples, before and after feeding the microbial addition. Nonetheless, microbial addition changed the abundance and structure of the microbiome in the digestive tract. Our data showed bovine yeast and LAB were beneficial for improving performance and regulating the microbial structure of dairy cows. This study was expected to enrich the knowledge of the digestive tract microbiome in dairy cows and provide a feasible strategy for the further utilization of bovine microorganisms.

Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future

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The inaccessible extreme environments harbor a large majority of anaerobic microbes which remain unknown.

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Anaerobic microbes are used in a variety of industrial applications.

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In the future, metagenomic-assisted techniques can be used to identify novel anaerobic microbes from the unexplored extreme environments.

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Genetic engineering can be used to enhance the efficiency of anaerobic microbes for various processes.

The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.

The Effect of Forage-to-Concentrate Ratio on Schizochytrium spp.-Supplemented Goats: Modifying Rumen Microbiota

Simple Summary

The in-depth understanding of rumen functions would be the greatest achievement of animal nutritionists. Hence, plenty of feed additives and various nutritional techniques are studied in modifying and understand the rumen habitat. In our study, we investigated the effect of alteration of the forage: concentrate (F:C) ratio in goats supplemented with the microalgae Schizochytrium spp. on rumen microbiota communities and enzymatic activity. Our results suggested that even though specific microbes’ abundance was altered, their corresponding enzymatic potential did not follow the same trend. Nonetheless, principal ruminal functions such as ammonia accumulation, fibrolytic activity, and degradation rate of specific fatty acids were also modified due to dietary intervention.

Abstract

The inclusion of feed additives and the implementation of various nutritional strategies are studied to modify the rumen microbiome and consequently its function. Nevertheless, rumen enzymatic activity and its intermediate products are not always matched with the microbiome structure. To further elucidate such differences a two-phase trial using twenty-two dairy goats was carried out. During the first phase, both groups (20HF n = 11; high forage and 20HG n = 11; high grain) were supplemented with 20 g Schizochytrium spp./goat/day. The 20HF group consumed a diet with a forage:concentrate (F:C) ratio of 60:40 and the 20HG-diet consisted of a F:C = 40:60. In the second phase, the supplementation level of Schizochytrium spp. was increased to 40 g/day/goat while the F:C ratio between the two groups were remained identical (40HF n = 11; high forage and 40HG n = 11; high grain). By utilizing a next-generation sequencing technology, we monitored that the high microalgae inclusion level and foremost in combination with a high grains diet increased the unmapped bacteria within the rumen. Bacteroidetes and Prevotella brevis were increased in the 40HG -fed goats as observed by using a qPCR platform. Additionally, methanogens and Methanomassiliicoccales were increased in high microalgae-fed goats, while Methanobrevibacter and Methanobacteriales were decreased. Fibrolytic bacteria were decreased in high microalgae-fed goats, while cellulolytic activity was increased. Ammonia was decreased in high grains-fed goats, while docosapentaenoic and docosahexaenoic acids showed a lower degradation rate in the rumen of high forage-fed goats. The alteration of the F:C ratio in goats supplemented with Schizochytrium spp. levels modified both ruminal microbiota and enzymatic activity. However, there was no significant consistency in the relations between them.

Identification of novel membrane proteins for improved lignocellulose conversion

Lignocellulose processing yields a heterogeneous mixture of substances, which are poorly utilized by current industrial strains. For efficient valorization of recalcitrant biomass, it is critical to identify and engineer new membrane proteins that enable the broad uptake of hydrolyzed substrates. Whereas glucose consumption rarely presents a bottleneck for cell factories, there is also a lack of transporters that allow co-consumption of glucose with other abundant biomass sugars such as xylose. This review discusses recent efforts to bioinformatically identify membrane proteins of high biotech potential for lignocellulose conversion and metabolic engineering in both model and nonconventional organisms. Of particular interest are transporters sourced from anaerobic gut fungi resident to large herbivores, which produce Sugars Will Eventually be Exported Transporters (SWEETs) that enhance xylose transport in the yeast Saccharomyces cerevisiae and enable glucose and xylose co-utilization. Additionally, recently identified fungal cellodextrin transporters are valuable alternatives to mitigate glucose repression and transporter inhibition.