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.

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.

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.

A successful workplace program for voluntary counseling and testing and treatment of HIV/AIDS at Heineken, Rwanda.

Heineken Breweries launched a workplace HIV/AIDS program at its Rwanda subsidiary in September 2001. By January 25, 2005, 736/2,595 eligible individuals had reported for counseling and HIV testing: 380/521 employees (72.9%), 254/412 spouses (61.7%), 99/1,517 children (6.5%), and 3/145 retired (2.0%). As a result, 109 HIV+ individuals were identified: 62 employees, 34 spouses, 12 children, and 1 retired. In September 2003 an anonymous HIV seroprevalence survey was performed with participation rates of 69.4% for employees, 58.2% for spouses, and 79.7% for adolescents. Using the survey result, the expected number of HIV+ employees was 71, which implies a program uptake of 87.1% (62/71) in this group. Of the identified 109 HIV+ beneficiaries, 42 were on highly active antiretroviral treatment (HAART). In November 2003 a qualitative study of awareness and health-seeking behavior of the Heineken Rwanda beneficiaries identified key principles contributing to the success of this program.

Public-private partnerships to build human capacity in low income countries: findings from the Pfizer program.

BACKGROUND: The ability of health organizations in developing countries to expand access to quality services depends in large part on organizational and human capacity. Capacity building includes professional development of staff, as well as efforts to create working environments conducive to high levels of performance. The current study evaluated an approach to public-private partnership where corporate volunteers give technical assistance to improve organizational and staff performance. From 2003 to 2005, the Pfizer Global Health Fellows program sent 72 employees to work with organizations in 19 countries. This evaluation was designed to assess program impact. METHODS: The researchers administered a survey to 60 Fellows and 48 Pfizer Supervisors. In addition, the team conducted over 100 interviews with partner organization staff and other key informants during site visits in Uganda, Kenya, Ghana, South Africa and India, the five countries where 60% of Fellows were placed. RESULTS: Over three-quarters of Fellowships appear to have imparted skills or enhanced operations of NGOs in HIV/AIDS and other health programs. Overall, 79% of Fellows reported meeting all or most technical assistance goals. Partner organization staff reported that the Fellows provided training to clinical and research personnel; strengthened laboratory, pharmacy, financial control, and human resource management systems; and helped expand Partner organization networks. Local staff also reported the Program changed their work habits and attitudes. The evaluation identified problems in defining goals of Fellowships and matching Organizations with Fellows. Capacity building success also appears related to size and sophistication of partner organization. CONCLUSION: Public expectations have grown regarding the role corporations should play in improving health systems in developing countries. Corporate philanthropy programs based on "donations" of personnel can help build the organizational and human capacity of frontline agencies delivering health services. More attention is needed to measure and compare outcomes of international volunteering programs, and to identify appropriate strategies for expansion.

"Spoiling the womb": definitions, aetiologies and responses to infertility in north west province, Cameroon.

Only one generation ago, the Cameroonian national population policy was pro-natalist, with great attention paid to the problem of sterility. Now, family planning is promoted nationwide to reduce population growth, and infertility is not addressed by public health policy or services. In contrast to the biomedical definition used by planners, at the local level infertility is defined as the inability to have a child when desired, and it has many causes including contraception, abortion and witchcraft. The young, less educated women especially are unlikely to use contraception as long as they feel susceptible to infertility, since their economic, social and psychological status hinge on their ability to have children. Drawing from epidemiological literature and qualitative data gathered in a market town in North West Province, I argue that a more balanced approach to reproductive health, one that recognises the importance of infertility, is critical for women's health and well-being.