Short-Term Belowground Responses to Thinning and Burning Treatments in Southwestern Ponderosa Pine Forests of the USA

Microbial-mediated decomposition and nutrient mineralization are major drivers of forest productivity. As landscape-scale fuel reduction treatments are being implemented throughout the fire-prone western United States of America, it is important to evaluate operationally how these wildfire mitigation treatments alter belowground processes. We quantified these important belowground components before and after management-applied fuel treatments of thinning alone, thinning combined with prescribed fire, and prescribed fire in ponderosa pine (Pinus ponderosa) stands at the Southwest Plateau, Fire and Fire Surrogate site, Arizona. Fuel treatments did not alter pH, total carbon and nitrogen (N) concentrations, or base cations of the forest floor (O horizon) or mineral soil (0–5 cm) during this 2-year study. In situ rates of net N mineralization and nitrification in the surface mineral soil (0–15 cm) increased 6 months after thinning with prescribed fire treatments; thinning only resulted in net N immobilization. The rates returned to pre-treatment levels after one year. Based on phospholipid fatty acid composition, microbial communities in treated areas were similar to untreated areas (control) in the surface organic horizon and mineral soil (0–5 cm) after treatments. Soil potential enzyme activities were not significantly altered by any of the three fuel treatments. Our results suggest that a variety of one-time alternative fuel treatments can reduce fire hazard without degrading soil fertility

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.T32GM008764 - NIGMS NIH HHS; T32 GM008764 - NIGMS NIH HHS; R01 DE024468 - NIDCR NIH HHS; R01 GM121950 - NIGMS NIH HHS; DE-SC0012627 - Biological and Environmental Research; RGP0020/2016 - Human Frontier Science Program; NSFOCE-BSF 1635070 - National Science Foundation; HR0011-15-C-0091 - Defense Advanced Research Projects Agency; R37DE016937 - NIDCR NIH HHS; R37 DE016937 - NIDCR NIH HHS; R01GM121950 - NIGMS NIH HHS; R01DE024468 - NIDCR NIH HHS; 1457695 - National Science FoundationPublished versio

Decomposition of coarse woody debris in a long-term litter manipulation experiment: A focus on nutrient availability

The majority of above-ground carbon in tropical forests is stored in wood, which is returned to the atmosphere during decomposition of coarse woody debris. However, the factors controlling wood decomposition have not been experimentally manipulated over time scales comparable to the length of this process.We hypothesized that wood decomposition is limited by nutrient availability and tested this hypothesis in a long-term litter addition and removal experiment in a lowland tropical forest in Panama. Specifically, we quantified decomposition using a 15-year chronosequence of decaying boles, and measured respiration rates and nutrient limitation of wood decomposer communities.The long-term probability that a dead tree completely decomposed was decreased in plots where litter was removed, but did not differ between litter addition and control treatments. Similarly, respiration rates of wood decomposer communities were greater in control treatments relative to litter removal plots; litter addition treatments did not differ from either of the other treatments. Respiration rates increased in response to nutrient addition (nitrogen, phosphorus, and potassium) in the litter removal and addition treatments, but not in the controls.Established decreases in concentrations of soil nutrients in litter removal plots and increased respiration rates in response to nutrient addition suggest that reduced rates of wood decomposition after litter removal were caused by decreased nutrient availability. The effects of litter manipulations differed directionally from a previous short-term decomposition study in the same plots, and reduced rates of bole decomposition in litter removal plots did not emerge until after more than 6 years of decomposition. These differences suggest that litter-mediated effects on nutrient dynamics have complex interactions with decomposition over time

A general framework for quantitatively assessing ecological stochasticity.

Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio (NST), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic (NST = 21%) to more stochastic (NST = 70%) right after organic carbon input. As the vegetable oil was consumed, the community gradually returned to be more deterministic (NST = 27%). In addition, our results demonstrated that null model algorithms and community similarity metrics had strong effects on quantifying ecological stochasticity

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species.

Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes.ImportanceDecades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems

The Ecological Factors that Structure the Composition and Function of Saprotrophic Fungi: Observational and Experimental Approaches.

A central goal in ecology is to understand the processes underlying the distribution and abundance of species at local, regional and global scales. As mediators of biogeochemical cycles, understanding the mechanisms that govern microbial community assembly are of ecosystem-scale significance, yet they remain a critical gap in our ecological knowledge. Through a combination of observational and experimental approaches, I explored the roles of selection, drift and dispersal in structuring microbial communities of saprotrophic fungi at a variety of spatial and temporal scales. Furthermore, I investigated the link between fungal community composition and functional characteristics in order to understand whether the factors that structure microbial community assembly have direct consequences to ecological function. First, I explored the role of selection in structuring soil microbial community assembly along a secondary successional chronosequence. My work revealed that the accumulation of organic matter and change in plant litter biochemistry during plant succession (10 to 86 yrs following agricultural abandonment) shaped saprotrophic fungal composition and their physiological potential to metabolize plant detritus, providing support for the idea that changes in plant communities have direct outcomes on the competitive dynamics of saprotrophic microbial communities in soil. Secondly, I found that both dispersal limitation and drift had a persistent effect on the phylogenetic structure and functional richness of saprotrophic fungal communities across a long-term glacial chronosequence (9,500 to 13,500 yrs following glacial retreat). Last, I manipulated initial colonizers and leaf litter biochemistry to understand the relative importance of priority effects and selection in structuring saprotrophic fungal communities and leaf litter decay. I found that the strength of priority effects was dependent on leaf litter biochemistry and physiological traits within a regional species pool. Together, these findings demonstrate that selection, drift and dispersal structure fungal community assembly at both local and regional levels with important consequences to plant litter decay. Furthermore, my observations provide support for the assertion that the same ecological forces structuring plant and animal communities also shape the assembly of saprotrophic fungi.PhDNatural Resources and EnvironmentUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113471/1/clinela_1.pd

Hyporheic invertebrates as bioindicators of ecological health in temporary rivers: a meta-analysis

Worldwide, many rivers cease flow and dry either naturally or owing to human activities such as water extraction. However, even when surface water is absent, diverse assemblages of aquatic invertebrates inhabit the saturated sediments below the river bed (hyporheic zone). In the absence of surface water or flow, biota of this zone may be sampled as an alternative to surface water-based ecological assessments. The potential of hyporheic invertebrates as ecological indicators of river health, however, is largely unexplored. We analysed hyporheic taxa lists from the international literature on temporary rivers to assess compositional similarity among broad-scale regions and sampling conditions, including the presence or absence of surface waters and flow, and the regional effect of hydrological phase (dry channel, non-flowing waters, surface flow) on richness. We hypothesised that if consistent patterns were found, then effects of human disturbances in temporary rivers may be assessable using hyporheic bioindicators. Assemblages differed geographically and by climate, but hydrological phase did not have a strong effect at the global scale. However, hyporheic assemblage composition within regions varied along a gradient of higher richness during wetter phases