Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment?

Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.

Ecology, adaptation, and function of methane-sulfidic spring water biofilm microorganisms, including a strain of anaerobic fungus Mucor hiemalis

Ecological aspects, adaptation, and some functions of a special biofilm and its unique key anaerobic fungus Mucor hiemalis strain EH11 isolated from a pristine spring (Künzing, Bavaria, Germany) are described. The spring's pure nature is characterized by, for example, bubbling methane, marine-salinity, mild hydrothermal (~19.1°C), sulfidic, and reductive-anoxic (Eh : -241 to -253 mV, O2 : ≤ 0.1 mg/L) conditions. It is geoecologically located at the border zone between Bavarian Forest (crystalline rocky mountains) and the moor-like Danube River valley, where geological displacements bring the spring's water from the deeper layers of former marine sources up to the surface. In the spring's outflow, a special biofilm with selective microorganisms consisting of archaea, bacteria, protozoa (ciliate), and fungus was found. Typical sulfidic-spring bryophyta and macrozoobenthos were missing, but many halo- and anaerotolerant diatoms and ciliate Vorticella microstoma beside EH11 were identified. Phase contrast and scanning electron microscopy revealed the existence of a stabilizing matrix in the biofilm formed by the sessile fungal hyphae and the exopolysaccharide substance (EPS) structures, which harbors other microorganisms. In response to ecological adaptation pressure caused by methane bubbles, EH11 developed an atypical spring-like hyphal morphology, similar to the spiral stalk of ciliate V. microstoma, to rise up with methane bubbles. For the first time, it was also demonstrated that under strict anaerobic conditions EH11 changes its asexual reproduction process by forming pseudosporangia via hyphal cell divisions as well as switching its metabolism to chemoautotrophic bacteria-like anaerobic life using acetate as an e-donor and ferrihydrite as an e-acceptor, all without fermentation. EH11 can be suggested to be useful for the microbial community in the Künzing biofilm not only due to its physical stabilization of the biofilm's matrix but also due to its ecological functions in element recycling as well as a remover of toxic metals.

Characterization of fungi from ruminal fluid of beef cattle with different ages and raised in tropical lignified pastures

The objective of this study was to evaluate the aerobic rumen mycobiota from three age groups of Nelore beef cattle reared extensively on lignified pasture. The experiment was randomized and sampled 50 steers, 50 cows, and 50 calves grazed on Brachiaria spp. pasture during the dry season. Rumen fluid in all animals was aromatic, slightly viscous, and greenish-brown in color. Microscopic examination revealed monocentric and polycentric anaerobic fungi in similar proportions (P > 0.05) in the rumen fluid of cows and steers. However, these microorganisms were not identified in any of the samples from calves. In culture exams, aerobic filamentous population was significantly higher for rumen fluid of cows compared to the other two groups. Microculture and rDNA sequence analyses showed Aspergillus spp. as the most frequent aerobic fungus among the isolates from the three bovine groups evaluated. Biochemical profiles were determined by the growth level of yeast isolates with 44 nutrient sources. Ten different yeast profiles were obtained, and yeast isolates from cow ruminal fluid showed ability to catabolize greater diversity of carbon and nitrogen sources. The differences in the fungal populations observed in this study could be explained by microbial and physiological interactions existing in the ruminal ecosystem of each age bovine group. The present study showed the fungal population of the rumen related with differences among age of cattle raised in lignified pastures. Metabolic capabilities of mycelial fungi or yeast identified in this study may be employed in new probiotics or microbial additives for different bovine categories.

Methods to study degradation of ruminant feeds

Ruman degradation is crucial in the supply of dietary nutrients to meet the nutrient demands of the anaerobic microbes and body tissues of ruminant animals. Therefore, it is essential to study the dynamics of rumen degradation of various feeds before their potential use to formulate nutritious diets for ruminant animals. Amongst many methods that have been used in the past, thein saccomethod has been the most effective method to study rumen degradation. However, this method is undesirable due to its implications for animal welfare and costs. While manyin vitromethods have been tested as possible alternatives to thein saccomethod to study rumen degradation of feeds, they were unable to remove the need to use fistulated animals to obtain rumen fluid. Although solubility, enzyme- and faeces-basedin vitromethods do not require rumen fluid, they still need data from either thein saccomethod or the rumen fluid-basedin vitromethods for comparison and validation. Therefore, there is a need to developin vitromethods that do not require the need to surgically modify ruminants to obtain rumen fluid to study rumen degradation. We review the potentials and problems associated with the existing methods to study rumen degradation and their implications for the animal industry in different situations.

Relative fibrolytic activities of anaerobic rumen fungi on untreated and sodium hydroxide treated barley straw in in vitro culture

The fibrolytic activities of rumen fungi were studied in terms of dry matter loss, plant cell wall degradation and enzyme (cellulase and xylanase) activities, when grown in vitro on either untreated or sodium hydroxide treated stems of barley straw over a 12 day period. Changes in fungal growth, development and overall biomass were followed using chitin assay and scanning electron microscopy. Treatment with sodium hydroxide resulted in a decrease in the NDF content together with the disruption of cuticle and the loosening and separation of the plant cells within the straw fragments. The enzyme activities of the anaerobic fungi have a high positive correlation (R(2)=0.99) with their biomass concentration assessed by chitin assay indicating that chitin is a valuable index for the estimation of the fungal biomass in vitro. The anaerobic fungi produced very extensive rhizoidal systems in these in vitro cultures. After incubation with rumen fungi, dry matter losses were, respectively, 35% and 38% for the untreated and treated straw samples and the overall fungal biomass, determined by chitin assay, was significantly higher in the treated samples. In vitro degradation of cellulose and hemicellulose was also higher in the treated than that of untreated cultures. Although, comparatively, xylanase activity was higher than that of cellulase, the cellulose fraction of the straw was degraded more than hemicellulose in both treated and untreated straw.

Methods for the isolation, culture and assessment of the status of anaerobic rumen chytrids in both in vitro and in vivo systems

Anaerobic fungi were isolated from both the rumen and faeces of nine sheep and a cow. A reliable and simple method for the isolation of anaerobic fungi using 24 h rumen incubated milled straw as the inoculum source was developed. We also evaluate the use of chitin measurements as an assay of rumen fungal biomass. Chitin levels were determined from various sample sources (milled barley straw used as the fungal culture substrate in vitro; plant particulate digests from the rumen (PLP) and centrifuged strained rumen fluid (CSRF) using both HPLC and colorimetric methods. Both methods were highly correlated and consequently the simpler colorimetric method was adopted for subsequent studies. There was also a high degree of correlation between anaerobic fungal cellulase activities with the assayed chitin content of milled barley straw cultures over 12 d of an in vitro experiment. The colorimetric chitin assay protocol was then used to assess the diurnal variation and abundance of rumen fungi in in vivo assays. We assessed the distribution of chitin (mg g(-1) dry matter) in various fractions of the strained rumen fluid (SRF) and PLP samples from the rumen of sheep. Chitin was detected in all fractions of strained rumen fluid but the main source of chitin in the samples may be attributed to the fungal biomass. We did not detect any significant differences in chitin levels over a 24 h sampling period. Finally, an SEM study on subsamples of milled straw and plant particulate matter used in the chitin assays, revealed that the pattern of the fungal development on substrate material differs from the culture medium to the rumen.