Species-specific coral microbiome assemblages support host bleaching resistance during an extreme marine heatwave.

Scleractinian assemblages are threatened by marine heat waves with coral survivorship depending on host genetics and microbiome composition. We documented an extreme marine heat wave in Fiji and the response of corals in two thermally stressed reef flats. Through high-throughput amplicon sequencing of 16S and ITS rDNA phylogenetic markers, we assessed coral microbiomes (Symbiodiniaceae, prokaryotes, fungi, and Apicomplexa) of paired bleached and unbleached colonies of four common coral species representative of dominant genera in the South Pacific.

The microbiome structure of decomposing plant leaves in soil depends on plant species, soil pore sizes, and soil moisture content.

Microbial communities are known as the primary decomposers of all the carbon accumulated in the soil. However, how important soil structure and its conventional or organic management, moisture content, and how different plant species impact this process are less understood. To answer these questions, we generated a soil microcosm with decomposing corn and soy leaves, as well as soil adjacent to the leaves, and compared it to control samples.

Interannual dynamics of Tuber melanosporum and fungal communities in productive black truffle orchards amended with truffle nests.

Truffle growers devote great efforts to improve black truffle productivity, developing agronomic practices such as 'truffle nests' (peat amendments that are supplemented with truffle spore inoculum). It has been hypothesized that improved fruiting associated with nests is linked to stimulation of truffle mycelia previously established in soil or to changes generated in soil fungal community. To assess this, we used real-time PCR to quantify black truffle extraradical mycelium during 2 years after nests installation.

Regional biogeography versus intra-annual dynamics of the root and soil microbiome.

Background: Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs.

Co-responses of bacterial and fungal communities to fire management treatments in Mediterranean pyrophytic ecosystems.

Cistus scrublands are pyrophytic ecosystems and occur widely across Mediterranean regions. Management of these scrublands is critical to prevent major disturbances, such as recurring wildfires. This is because management appears to compromise the synergies necessary for forest health and the provision of ecosystem services.

Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management.

Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems.

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche.

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities.

Host genotype controls ecological change in the leaf fungal microbiome.

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics.

Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly.

Switchgrass () is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple.

CONSTAX2: improved taxonomic classification of environmental DNA markers.

Summary: CONSTAX-the CONSensus TAXonomy classifier-was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials.

Effect of earthworms on mycorrhization, root morphology and biomass of silver fir seedlings inoculated with black summer truffle (Tuber aestivum Vittad.).

Species of the genus Tuber have gained a lot of attention in recent decades due to their aromatic hypogenous fruitbodies, which can bring high prices on the market. The tendency in truffle production is to infect oak, hazel, beech, etc. in greenhouse conditions.

Lack of Linkages among Fruiting Depth, Weight, and Maturity in Irrigated Truffle Fungi Marks the Complexity of Relationships among Morphogenetic Stages.

The highly prized black truffle () has become a model species for ectomycorrhizal fungi biology. However, several questions concerning its reproductive phase remain unanswered. To provide new hypotheses on the fruitbody formation process, we have explored the causal links among development characters of black truffle fruitbodies that are primarily linked to either the mating process, fruitbody growing stage, or maturation.

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities?

Soil archives are an important resource in agronomic and ecosystem sciences. If microbial communities could be reconstructed from archived soil DNA, as prehistoric plant communities are reconstructed via pollen data, soil archive resources would assume even greater value for reconstructing land-use history, forensic science, and biosphere modelling. Yet, the effects of long-term soil archival on the preservation of microbial DNA is still largely unknown.

Crop Management Impacts the Soybean () Microbiome.

Soybean () is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop.

Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi.

Lycopods are tracheophytes in the Kingdom Plantae and represent one of the oldest lineages of living vascular plants. Symbiotic interactions between these plants with fungi and bacteria, including fine root endophytes in Endogonales, have been hypothesized to have helped early diverging plant lineages colonize land. However, attempts to study the lycopod rhizobiome in its natural environment are still limited.

Draft Genome Sequence of the Ectomycorrhizal Ascomycete .

is a pioneer ectomycorrhizal fungus with facultative saprophytic capacities. Here, we sequenced the genome of strain Sb_GMNB300, which is estimated at 51.6 Mb in size with 872 assembled contigs accounting for 12,597 predicted coding genes.

Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors.

Morel mushrooms (Morchella, Pezizales) are highly prized edible fungi. Approaches to cultivate morels indoors in pasteurized composted substrates have been successful for Morchella rufobrunnea. We used DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) ribosomal DNA and 16S rRNA gene to follow bacterial and fungal communities in substrates during indoor morel cultivation.

Microbial communities associated with the black morel cultivated in greenhouses.

Morels ( spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi.

Fungal-Bacterial Networks in the Rhizobiome Are Impacted by Soil Properties and Host Genotype.

Plant root-associated microbial symbionts comprise the plant rhizobiome. These microbes function in provisioning nutrients and water to their hosts, impacting plant health and disease. The plant microbiome is shaped by plant species, plant genotype, soil and environmental conditions, but the contributions of these variables are hard to disentangle from each other in natural systems.

Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific.

The Fiji Islands is an archipelago of more than 330 islands located in the tropics of the South Pacific Ocean. Microbial diversity and biogeography in this region is still not understood. Here, we present the first molecular characterization of fungal, bacterial, and archaeal communities in soils from different habitats within the largest Fijian island, Viti Levu.

Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle.

Bacterial interactions with animals and plants have been examined for over a century; by contrast, the study of bacterial-fungal interactions has received less attention. Bacteria interact with fungi in diverse ways, and endobacteria that reside inside fungal cells represent the most intimate interaction. The most significant bacterial endosymbionts that have been studied are associated with Mucoromycota and include two main groups: Burkholderia-related and Mycoplasma-related endobacteria (MRE).

CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences.

Background: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies.

Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.

Illumina amplicon sequencing of soil in a temperate pine forest in the southeastern United States detected an abundant, nitrogen (N)-responsive fungal genotype of unknown phylogenetic affiliation. Two isolates with ribosomal sequences consistent with that genotype were subsequently obtained. Examination of records in GenBank revealed that a genetically similar fungus had been isolated previously as an endophyte of moss in a pine forest in the southwestern United States.