Temperate trees locally engineer decomposition and litter-bound microbiomes through differential litter deposits and species-specific soil conditioning.

Leaf decomposition varies widely across temperate forests, shaped by factors like litter quality, climate, soil properties, and decomposers, but forest heterogeneity may mask local tree influences on decomposition and litter-associated microbiomes. We used a 24-yr-old common garden forest to quantify local soil conditioning impacts on decomposition and litter microbiology. We introduced leaf litter bags from 10 tree species (5 arbuscular mycorrhizal; 5 ectomycorrhizal) to soil plots conditioned by all 10 species in a full-factorial design. After 6 months, we assessed litter mass loss, C/N content, and bacterial and fungal composition. We hypothesized that (1) decomposition and litter-associated microbiome composition would be primarily shaped by the mycorrhizal type of litter-producing trees, but (2) modified significantly by underlying soil, based on mycorrhizal type of the conditioning trees. Decomposition and, to a lesser extent, litter-associated microbiome composition, were primarily influenced by the mycorrhizal type of litter-producing trees. Interestingly, however, underlying soils had a significant secondary influence, driven mainly by tree species, not mycorrhizal type. This secondary influence was strongest under trees from the Pinaceae. Temperate trees can locally influence underlying soil to alter decomposition and litter-associated microbiology. Understanding the strength of this effect will help predict biogeochemical responses to forest compositional change.

Contaminant Biomagnification in Polar Bears: Interindividual Differences, Dietary Intake Rate, and the Gut Microbiome.

Some persistent hydrophobic pollutants biomagnify, i.e., achieve higher contaminant levels in a predator than in its prey (Cpredator/Cprey > 1). This ratio is called the biomagnification factor (BMF) and is traditionally determined using tissues from carcasses or biopsies. Using a noninvasive method that relies on equilibrium sampling in silicone-film-coated vessels and chemical analysis of paired diet and feces, we determined on three occasions the thermodynamic biomagnification limit (BMFlim) and feces-based biomagnification factor (BMFF) for three zoo-housed polar bears who experience seasonal periods of hyperphagia and hypophagia. All bears had high biomagnification capabilities (BMFlim was up to 200) owing to very efficient lipid assimilation (up to 99.5%). The bears differed up to a factor of 3 in their BMFlim. BMFlim and BMFF of a bear increased by up to a factor of 4 during the hypophagic period, when the ingestion rate was greatly reduced. Much of that variability can be explained by differences in the lipid assimilation efficiency, even though this efficiency ranged only from 98.1 to 99.5%. A high BMFlim was associated with a high abundance of Bacteroidales and Lachnospirales in the gut microbiome. Biomagnification varies to a surprisingly large extent between individuals and within the same individual over time. Future work should investigate whether this can be attributed to the influence of the gut microbiome on lipid assimilation by studying more individual bears at different key physiological stages.

Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists.

Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.

Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites.

Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.

Leveraging microbiome rediversification for the ecological rescue of soil function.

BACKGROUND: Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples. RESULTS: Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions. CONCLUSIONS: In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.

Shared and unique responses in the microbiome of allopatric lizards reared in a standardized environment.

The gut microbiome can influence host fitness and, consequently, the ecology and evolution of natural populations. Microbiome composition can be driven by environmental exposure but also by the host's genetic background and phenotype. To contrast environmental and genetic effects on the microbiome we leverage preserved specimens of eastern fence lizards from allopatric lineages east and west of the Mississippi River but reared in standardized conditions. Bacterial composition was indistinguishable between lineages but responded significantly to host age-a proxy for environmental exposure. This was accompanied by a continuous decrease in bacterial diversity in both lineages, partially driven by decreasing evenness seen only in western lizards. These findings indicate that longer exposure to a homogeneous habitat may have a depreciating effect on microbiome diversity in eastern fence lizards, a response shared by both lineages. We highlight the importance of such effects when extrapolating patterns from laboratory experiments to the natural world.

Functionally-explicit sampling can answer key questions about the specificity of plant-microbe interactions.

The rhizosphere is a nexus for plant-microbe interactions and, as a host-structured environment, a location of high activity for distinct microbes and plant species. Although our insights into this habitat have exploded in recent years, we are still limited in our ability to answer key questions about the specificity of these root-microbial relationships. In particular, it can be difficult to confirm or reject microbiome heritability in many plant systems and to pinpoint which microbial taxa are key to plant functioning. Like other host-structured environments, the rhizosphere is structurally, chemically, and biologically complex, driven largely by differences in root anatomy, location, and function. In this Correspondence, we describe a review of 377 "rhizosphere microbiome" research papers and demonstrate how matching a sampling method to the biological question can advance our understanding of host-microbe interactions in a functionally heterogeneous environment. We found that the vast majority of studies (92%) pool all roots from a root system during sampling, ignoring variation in microbial composition between roots of different function and limiting insight into key root-microbial relationships. Furthermore, approaches for removing root-associated microbes are highly variable and non-standard, complicating multi-study analyses. Our understanding of the strength and nature of host-microbe relationships in heterogenous host-microbiome environments can be clarified by targeting sampling to locations of high interaction. While the high complexity of the rhizosphere creates logistical challenges, we suggest that unambiguous language and refined approaches will improve our ability to match methods to research questions and advance our understanding of the specificity of plant-microbial interactions.

Farm-scale differentiation of active microbial colonizers.

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.

Phylogenetic Signal, Root Morphology, Mycorrhizal Type, and Macroinvertebrate Exclusion: Exploring Wood Decomposition in Soils Conditioned by 13 Temperate Tree Species.

Woodlands are pivotal to carbon stocks, but the process of cycling C is slow and may be most effective in the biodiverse root zone. How the root zone impacts plants has been widely examined over the past few decades, but the role of the root zone in decomposition is understudied. Here, we examined how mycorrhizal association and macroinvertebrate activity influences wood decomposition across diverse tree species. Within the root zone of six predominantly arbuscular mycorrhizal (AM) (Acer negundo, Acer saccharum, Prunus serotina, Juglans nigra, Sassafras albidum, and Liriodendron tulipfera) and seven predominantly ectomycorrhizal (EM) tree species (Carya glabra, Quercus alba, Quercus rubra, Betula alleghaniensis, Picea rubens, Pinus virginiana, and Pinus strobus), woody litter was buried for 13 months. Macroinvertebrate access to woody substrate was either prevented or not using 0.22 mm mesh in a common garden site in central Pennsylvania. Decomposition was assessed as proportionate mass loss, as explained by root diameter, phylogenetic signal, mycorrhizal type, canopy tree trait, or macroinvertebrate exclusion. Macroinvertebrate exclusion significantly increased wood decomposition by 5.9%, while mycorrhizal type did not affect wood decomposition, nor did canopy traits (i.e., broad leaves versus pine needles). Interestingly, there was a phylogenetic signal for wood decomposition. Local indicators for phylogenetic associations (LIPA) determined high values of sensitivity value in Pinus and Picea genera, while Carya, Juglans, Betula, and Prunus yielded low values of sensitivity. Phylogenetic signals went undetected for tree root morphology. Despite this, roots greater than 0.35 mm significantly increased woody litter decomposition by 8%. In conclusion, the findings of this study suggest trees with larger root diameters can accelerate C cycling, as can trees associated with certain phylogenetic clades. In addition, root zone macroinvertebrates can potentially limit woody C cycling, while mycorrhizal type does not play a significant role.

Can dispersal be leveraged to improve microbial inoculant success?

Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.

Soil salinization accelerates microbiome stabilization in iterative selections for plant performance.

Climate change-related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so diverse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants. In both salt-amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high-biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add-back control (re-adding initial frozen soil microbiome) as a within-generation reference for microbiome and plant phenotype selection. We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently diverged from the add-back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued. These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes.

Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition.

The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield.

The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering.

Fine roots vary dramatically in their functions, which range from resource absorption to within-plant resource transport. These differences should alter resource availability to root-associated microorganisms, yet most root microbiome studies involve fine root homogenization. We hypothesized that microbial filtering would be greatest in the most distal roots. To test this, we sampled roots of six temperate tree species from a 23-year-old common garden planting, separating by branching order. Rhizoplane bacterial composition was characterized with 16S rRNA gene sequencing, while bacterial abundance was determined on a subset of trees through flow cytometry. Root order strongly impacted composition across tree species, with absorptive lower order roots exerting the greatest selective pressure. Microbial carrying capacity was higher in absorptive roots in two of three tested tree species. This study indicates lower order roots as the main point of microbial interaction with fine roots, suggesting that root homogenization could mask microbial recruitment signatures.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection.

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Abiotic conditions outweigh microbial origin during bacterial assembly in soils.

Understanding the processes guiding microbial community assembly in soils is essential for predicting microbiome structure and function following soil disturbance events like agricultural soil fumigation. However, assembly outcomes are complex and variable, being affected by both selective abiotic forces and by the history of colonizing microorganisms. To untangle the interactions between these factors, we conducted a controlled microcosm study tracking bacterial assembly in cleared soils over 7 weeks. We used mesh bags to connect five unsterilized source soils, differing in land use history (forested, agricultural, or fallow), with four sterile recipient soil treatments, differing in abiotic conditions (no soil additives, salt addition, urea addition, or mixed salt/urea addition). We found that 59%-96% of bacterial colonizers after 1 week were Firmicutes, but by 7 weeks Actinobacteria and Bacteroidetes were also dominant. Salt and nitrogen additions reshaped bacterial assembly by constraining alpha diversity by up to half and biomass accumulation by up to an order of magnitude. Within-treatment dispersion was significantly lower for salt and nutrient addition microcosms, suggesting deterministic selective pressures. In contrast, source soil origin had little impact on assembly trajectories. These results suggest that abiotic conditions can overshadow microbial source history in shaping community assembly outcomes.

Many roads to bacterial generalism.

The fundamental niches of bacteria can be defined along many environmental axes, including temperature tolerance and resources consumed, while interactions with other organisms can constrain (e.g. competition) or enlarge (e.g. cross-feeding) realized niches. Organisms are often categorized as generalists or specialists, corresponding to broad or narrow niche requirements, which can then be linked to their functional role in an ecosystem. We show how these terms are applied to bacteria, make predictions about how the type and extent of generalism displayed by an organism relates to its functional potential and discuss the value of collecting different types of generalist bacteria. We believe that new approaches that take advantage of both high-throughput sequencing and environmental manipulation can allow us to understand the many types of generalism found within both cultivated and yet-to-be-cultivated bacteria.

Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea.

Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer.

Experimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through (i) direct soil transfer at two dilutions and (ii) a new approach, sustained contact between source and recipient soils. Sustained soil-to-soil contact retains separation between source and recipient soils, allows for multiple colonization events and increases confidence that microorganisms observed in recipient soils are active and growing. Each approach produced distinct microbiomes in recipient soils after 1 and 6 weeks of incubation, indicating that transfer method impacts microbial composition. The extent to which recipient microbiomes resembled source microbiomes varied by soil type, although in general, direct soil transfer appeared to most closely approximate source microbiomes. However, irrespective of transfer method, most bacterial sequences in recipient soils were from organisms transferred through all methods. We discuss the merits of each method for controlled soil microbiome studies.

100 Years Since Tolaas: Bacterial Blotch of Mushrooms in the 21st Century.

Among the biotic constraints of common mushroom (Agaricus bisporus) production, bacterial blotch is considered the most important mushroom disease in terms of global prevalence and economic impact. Etiology and management of bacterial blotch has been a major concern since its original description in 1915. Although Pseudomonas tolaasii is thought to be the main causal agent, various Pseudomonas species, as well as organisms from other genera have been reported to cause blotch symptoms on mushroom caps. In this review, we provide an updated overview on the etiology, epidemiology, and management strategies of bacterial blotch disease. First, diversity of the causal agent(s) and utility of high throughput sequencing-based approaches in the precise characterization and identification of blotch pathogen(s) is explained. Further, due to the limited options for use of conventional pesticides in mushroom farms against blotch pathogen(s), we highlight the role of balanced threshold of relative humidity and temperature in mushroom farms to combat the disease in organic and conventional production. Additionally, we discuss the possibility of the use of biological control agents (either antagonistic mushroom-associated bacterial strains or bacteriophages) for blotch management as one of the sustainable approaches for 21st century agriculture. Finally, we aim to elucidate the association of mushroom microbiome in cap development and productivity on one hand, and blotch incidence/outbreaks on the other hand.