Biochar is colonized by select arbuscular mycorrhizal fungi in agricultural soils.

Arbuscular mycorrhizal fungi (AMF) colonize biochar in soils, yet the processes governing their colonization and growth in biochar are not well characterized. Biochar amendment improves soil health by increasing soil carbon, decreasing bulk density, and improving soil water retention, all of which can increase yield and alleviate environmental stress on crops. Biochar is often applied with nutrient addition, impacting mycorrhizal communities. To understand how mycorrhizas explore soils containing biochar, we buried packets of non-activated biochar in root exclusion mesh bags in contrasting agricultural soils. In this greenhouse experiment, with quinoa (Chenopodium quinoa) as the host plant, we tested impacts of mineral nutrient (as manure and fertilizer) and biochar addition on mycorrhizal colonization of biochar. Paraglomus appeared to dominate the biochar packets, and the community of AMF found in the biochar was a subset (12 of 18) of the virtual taxa detected in soil communities. We saw differences in AMF community composition between soils with different edaphic properties, and while nutrient addition shifted those communities, the shifts were inconsistent between soil types and did not significantly influence the observation that Paraglomus appeared to selectively colonize biochar. This observation may reflect differences in AMF traits, with Paraglomus previously identified only in soils (not in roots) pointing to predominately soil exploratory traits. Conversely, the absence of some AMF from the biochar implies either a reduced tendency to explore soils or an ability to avoid recalcitrant nutrient sources. Our results point to a selective colonization of biochar in agricultural soils.

Mycorrhizas transfer carbon in a mature mixed forest.

Mycorrhizal fungi transfer nutrients to plants in exchange for photosynthates. Plants allocate up to 20% of their carbon to mycorrhizal structures, mycelium and fruit bodies of their fungal partners. Individuals of mycorrhizal fungi may encompass hundreds of square metres of soil and defragmented litter, linking multiple plant individuals of different species and size (Figure 1). Using a free-air 13 CO2 enrichment (web-FACE) technique in a mature forest, interspecific transfer accounted for 40% of fine root carbon after 5 years of back and forth transfer between trees. In this issue of Molecular Ecology, Rog, Rosenstock, Körner, and Klein (2020) show that closely related trees shared relatively more mycorrhizal fungi than distantly related trees in the same experimental site, which correlated to increased carbon sharing.

Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts.

Arbuscular mycorrhizal fungi (AMF) are globally distributed, monophyletic root symbionts with ancient origins. Their contribution to carbon cycling and nutrient dynamics is ecologically important, given their obligate association with over 70% of vascular plant species. Current understanding of AMF species richness and community structure is based primarily on studies of grasses, herbs and agricultural crops, typically in disturbed environments. Few studies have considered AMF interactions with long-lived woody perennial species in undisturbed ecosystems. Here we examined AMF communities associated with roots and soils of young, mature and old western redcedar (Thuja plicata) at two sites in the old-growth temperate rainforests of British Columbia. Due to the unique biology of AMF, community richness and structure were assessed using a conservative, clade-based approach. We found 91 AMF OTUs across all samples, with significantly greater AMF richness in the southern site, but no differences in richness along the host chronosequence at either site. All host age classes harboured AMF communities that were overdispersed (more different to each other than expected by chance), with young tree communities most resembling old tree communities. A comparison with similar clade richness data obtained from the literature indicates that western redcedar AMF communities are as rich as those of grasses, tropical trees and palms. Our examination of undisturbed temperate old-growth rainforests suggests that priority effects, rather than succession, are an important aspect of AMF community assembly in this ecosystem.

Host and habitat filtering in seedling root-associated fungal communities: taxonomic and functional diversity are altered in 'novel' soils.

Climatic and land use changes have significant consequences for the distribution of tree species, both through natural dispersal processes and following management prescriptions. Responses to these changes will be expressed most strongly in seedlings near current species range boundaries. In northern temperate forest ecosystems, where changes are already being observed, ectomycorrhizal fungi contribute significantly to successful tree establishment. We hypothesised that communities of fungal symbionts might therefore play a role in facilitating, or limiting, host seedling range expansion. To test this hypothesis, ectomycorrhizal communities of interior Douglas-fir and interior lodgepole pine seedlings were analysed in a common greenhouse environment following growth in five soils collected along an ecosystem gradient. Currently, Douglas-fir's natural distribution encompasses three of the five soils, whereas lodgepole pine's extends much further north. Host filtering was evident amongst the 29 fungal species encountered: 7 were shared, 9 exclusive to Douglas-fir and 13 exclusive to lodgepole pine. Seedlings of both host species formed symbioses with each soil fungal community, thus Douglas-fir did so even where those soils came from outside its current distribution. However, these latter communities displayed significant taxonomic and functional differences to those found within the host distribution, indicative of habitat filtering. In contrast, lodgepole pine fungal communities displayed high functional similarity across the soil gradient. Taxonomic and/or functional shifts in Douglas-fir fungal communities may prove ecologically significant during the predicted northward migration of this species; especially in combination with changes in climate and management operations, such as seed transfer across geographical regions for forestry purposes.

Arbuscular mycorrhizal fungi in oat-pea intercropping.

Arbuscular mycorrhizal fungal diversity can be altered by intercropping plant species, as well as N fertilizer applications. This study examined the effects of oat-pea intercropping and N fertilizer addition on the richness and diversity of mycorrhizal species, as well as identified the most common arbuscular mycorrhizal fungi (AMF) genera recruited for oats and peas in two growing seasons (2019 and 2020). The AMF diversity was higher in an intercropped system compared to their respective monocropping system. Under drier conditions in 2019, arbuscular mycorrhizal richness decreased with N fertilizer addition in sole peas and increased with N fertilizer addition in sole oats, but no significant change in richness was observed in oat-pea intercropping. During the wetter growing season 2020, arbuscular mycorrhizal diversity increased when oat and pea were intercropped, compared to either sole oat or sole pea. Diversispora in sole pea was a significant indicator differentiating the root associated AMF community from sole oat. Claroideoglomus richness increased in peas in 2020, thus this genus could be moisture dependent. Paraglomus richness in oat-pea intercropping was similar to sole oat in 2019, and similar to sole pea in 2020. This can suggest that Paraglomus is an indicator of plant stress under intercropping, as based on the premise that stressed plants release more exudates, and the subsequent mycorrhizal associations favor these plants with higher exudation. Future investigations can further reveal the functions and benefits of these mycorrhizal genera in annual monocrop and intercropping systems.

Effects of feeding a pine-based biochar to beef cattle on subsequent manure nutrients, organic matter composition and greenhouse gas emissions.

Biochar in ruminant diets is being assessed as a method for simultaneously improving animal production and reducing enteric CH4 emissions, but little is known about subsequent biochar-manure interactions post-excretion. We examined chemical properties, greenhouse gas (GHG) emissions and organic matter (OM) composition during farm scale stockpiling (SP) or composting (CP) of manure from cattle that either received a pine-based biochar in their diet (BM) or did not (RM). Manure piles were monitored hourly for temperature and weekly for top surface CO2, N2O and CH4 fluxes over 90 d in a semiarid location near Lethbridge, AB, Canada. Results indicate that cumulative CO2, N2O and CH4 emissions were not affected by biochar, implying that BM was as labile as RM. The pH, total C (TC), NO3-N and Olsen P were also not influenced by biochar, although it was observed that NH4-N and OM extractability were both 13% lower in BM than RM. Solid-state 13C nuclear magnetic resonance (NMR) showed that biochar increased stockpile/compost aromaticity, yet it did not alter the bulk C speciation of manure OM. Further analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed that dissolved OM was enriched by strongly reduced chemical constituents, with BM providing more humic-like OM precursors than RM. Inclusion of a pine-based biochar in cattle diets to generate BM is consistent with current trends in the circular economy, "closing the loop" in agricultural supply chains by returning C-rich organic amendments to croplands. Stockpiling/composting the resulting BM, however, may not provide a clear advantage over directly mixing low levels of biochar with manure. Further research is required to validate BM as a tool to reduce the C footprint of livestock waste management.

Maternal Intake of Dietary Fat Pre-Programs Offspring's Gut Ecosystem Altering Colonization Resistance and Immunity to Infectious Colitis in Mice.

SCOPE: The transgenerational impact of dietary fat remains unclear. Here, the role of maternal fat consumption as a modulator of gut microbial communities and infectious disease outcomes in their offspring is explored. METHODS AND RESULTS: C57BL/6 mice are fed isocaloric high-fat diets throughout breeding, gestation and lactation. Diets contained either milk fat (MF), olive oil (OO) or corn oil (CO), with or without fish oil. The pups born to maternally exposed mice are weaned on to chow and raised into adulthood. At 8 weeks, the offsprings are either euthanized for colonic 16S rRNA analysis or challenged with the enteric pathogen, Citrobacter rodentium. Maternal CO exposure resulted in unique clustering of bacterial communities in offspring compared with MF and OO. Diets rich in CO reduced survival in offspring challenged with C. rodentium. The addition of fish oil did not improve mortality caused by CO and worsened disease outcomes when combined with OO. Unlike the unsaturated diets, MF is protective with and without fish oil. CONCLUSIONS: Overall, these data reveal that maternal intake of fatty acids do have transgenerational impacts on their offspring's bacteriome and enteric infection risk. Based on this study, saturated fats should be included in maternal diets.

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice.

Accumulating evidence supports that the intestinal microbiome is involved in Type 1 diabetes (T1D) pathogenesis through the gut-pancreas nexus. Our aim was to determine whether the intestinal microbiota in the non-obese diabetic (NOD) mouse model played a role in T1D through the gut. To examine the effect of the intestinal microbiota on T1D onset, we manipulated gut microbes by: (1) the fecal transplantation between non-obese diabetic (NOD) and resistant (NOR) mice and (2) the oral antibiotic and probiotic treatment of NOD mice. We monitored diabetes onset, quantified CD4+T cells in the Peyer's patches, profiled the microbiome and measured fecal short-chain fatty acids (SCFA). The gut microbiota from NOD mice harbored more pathobionts and fewer beneficial microbes in comparison with NOR mice. Fecal transplantation of NOD microbes induced insulitis in NOR hosts suggesting that the NOD microbiome is diabetogenic. Moreover, antibiotic exposure accelerated diabetes onset in NOD mice accompanied by increased T-helper type 1 (Th1) and reduced Th17 cells in the intestinal lymphoid tissues. The diabetogenic microbiome was characterized by a metagenome altered in several metabolic gene clusters. Furthermore, diabetes susceptibility correlated with reduced fecal SCFAs. In an attempt to correct the diabetogenic microbiome, we administered VLS#3 probiotics to NOD mice but found that VSL#3 colonized the intestine poorly and did not delay diabetes. We conclude that NOD mice harbor gut microbes that induce diabetes and that their diabetogenic microbiome can be amplified early in life through antibiotic exposure. Protective microbes like VSL#3 are insufficient to overcome the effects of a diabetogenic microbiome.

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool.

Gut microbiome community analysis is used to understand many diseases like inflammatory bowel disease, obesity, and diabetes. Sampling methods are an important consideration for human microbiome research, yet are not emphasized in many studies. In this study, we demonstrate that the preparation, handling, and storage of human faeces are critical processes that alter the outcomes of downstream DNA-based bacterial community analyses via qPCR. We found that stool subsampling resulted in large variability of gut microbiome data due to different microenvironments harbouring various taxa within an individual stool. However, we reduced intra-sample variability by homogenizing the entire stool sample in liquid nitrogen and subsampling from the resulting crushed powder prior to DNA extraction. We experimentally determined that the bacterial taxa varied with room temperature storage beyond 15 minutes and beyond three days storage in a domestic frost-free freezer. While freeze thawing only had an effect on bacterial taxa abundance beyond four cycles, the use of samples stored in RNAlater should be avoided as overall DNA yields were reduced as well as the detection of bacterial taxa. Overall we provide solutions for processing and storing human stool samples that reduce variability of microbiome data. We recommend that stool is frozen within 15 minutes of being defecated, stored in a domestic frost-free freezer for less than three days, and homogenized prior to DNA extraction. Adoption of these simple protocols will have a significant and positive impact on future human microbiome research.

Inter-plant communication through mycorrhizal networks mediates complex adaptive behaviour in plant communities.

Adaptive behaviour of plants, including rapid changes in physiology, gene regulation and defence response, can be altered when linked to neighbouring plants by a mycorrhizal network (MN). Mechanisms underlying the behavioural changes include mycorrhizal fungal colonization by the MN or interplant communication via transfer of nutrients, defence signals or allelochemicals. We focus this review on our new findings in ectomycorrhizal ecosystems, and also review recent advances in arbuscular mycorrhizal systems. We have found that the behavioural changes in ectomycorrhizal plants depend on environmental cues, the identity of the plant neighbour and the characteristics of the MN. The hierarchical integration of this phenomenon with other biological networks at broader scales in forest ecosystems, and the consequences we have observed when it is interrupted, indicate that underground 'tree talk' is a foundational process in the complex adaptive nature of forest ecosystems.

Molecular approaches for AM fungal community ecology: A primer.

Molecular techniques are no longer optional for ecologists interested in arbuscular mycorrhizal (AM) communities. Understanding the role of these soil fungi in natural systems requires knowledge of their abundance and identity but this is impossible to achieve without a molecular approach. Adapting molecular tools to AM fungi can be challenging because of the unique biology of the fungi. Moreover, many recruits in the field of mycorrhizal ecology have little or no experience with molecular biology. Here, we outline a conceptual framework for designing robust ecological experiments with AM fungi using molecular approaches.