Seeing the forest for the trees: Tree species effects on soil microbial communities and nutrient cycling dynamics

Tree species influence soils above and belowground communities through leaf litter and root inputs. Soil microbial communities can directly influence tree growth and development through processes such as decomposition of leaves, and indirectly through chemical transformation of nutrients in soils as an influence of altered C:N ratios due to leaf litter and root inputs. This thesis aims to document some of the mechanisms by which trees influence soil microbial communities and nitrogen cycling processes like gross and net ammonification and nitrification. This thesis also aims to determine the role of site nitrogen status in modulating those tree species effects. The effects of tree species on ammonification and nitrification rates in forest floors and mineral soils were explored, and related to functional genetic markers for ammonia-oxidation by archaea and bacteria (amoA AOA and AOB), bacterial denitrification (nirS and nirK), and the general markers for bacteria (16S) and fungi (ITS). Two paired high-resolution laboratory methods were used to investigate the relationships between trees, soils, and the microbial communities, including molecular techniques such as quantitative polymerase chain reaction (qPCR) to target gene abundances in soils, and 15N pool-dilution experiments to understand how ammonium and nitrate are produced and consumed in soils. Soil samples were collected from two common garden experiments, named EP571 in Canada (Ribbons et al. 2016), and in Denmark, and both 15N and qPCR-based techniques were used to determine tree species effects and attribute N cycling processes to the abundances of functional genes. At EP571, western red cedar (Thuja plicata) forest floor nitrogen transformation rates differed from Douglas-fir (Pseudotsuga menziesii), Sitka spruce (Picea sitchensis), and western hemlock (Tsuga heterophylla), which corresponded with western red cedar having highest abundances of bacterial 16S and amoA AOA genes. A manipulative mesocosm (the Rhizotron) in Wales was used to determine how mixtures and monocultures of seedling species influenced tree growth, soil physical properties and soil microbial community structure and function within the first three years of growth. Within the Rhizotron experiment both alder (Alnus rubra) and Douglas-fir grew taller when grown in mixtures compared with monocultures of each species. Sycamore maple (Acer pseudoplatanus) acquired slightly greater aboveground biomass when planted in mixtures with common oak (Quercus robur), which attained less biomass in mixtures than monocultures. C:N ratios of leaves, stems, roots, and rhizospheric soils were determined to see if mixtures influenced C:N in trees. Rhizospheric soil microbial communities (including bacterial and fungal markers and the 4 genes tied to N cycling) were compared among the 4 tree species in the Rhizotron. Soil samples for microbial analyses were collected before seedlings were planted, and just before the experiment was harvested. These data show differences in height, biomass and C:N ratios between species can be observed at a seedling growth stage, but microbial communities may require longer exposure to develop. Lastly, the Bangor Diverse experiment was used to further explore diversity and mixture effects on soil microbial communities and N transformations. We found few mixture or monoculture tree species effects on mineral soil microbial communities or net nitrification or ammonification rates. Collectively, these stories shed light on the important functional role of soil microbes in forest soil N cycling. This thesis also highlights the use of isotope and microbial techniques for parsing out relationships between site, tree species identity and ecosystem functions, with the largest links observed between gross ammonification and microbial communities

Ant-mediated seed dispersal in a warmed world

Climate change affects communities both directly and indirectly via changes in interspecific interactions. One such interaction that may be altered under climate change is the ant-plant seed dispersal mutualism common in deciduous forests of eastern North America. As climatic warming alters the abundance and activity levels of ants, the potential exists for shifts in rates of ant-mediated seed dispersal. We used an experimental temperature manipulation at two sites in the eastern US (Harvard Forest in Massachusetts and Duke Forest in North Carolina) to examine the potential impacts of climatic warming on overall rates of seed dispersal (using Asarum canadense seeds) as well as species-specific rates of seed dispersal at the Duke Forest site. We also examined the relationship between ant critical thermal maxima (CTmax) and the mean seed removal temperature for each ant species. We found that seed removal rates did not change as a result of experimental warming at either study site, nor were there any changes in species-specific rates of seed dispersal. There was, however, a positive relationship between CTmax and mean seed removal temperature, whereby species with higher CTmax removed more seeds at hotter temperatures. The temperature at which seeds were removed was influenced by experimental warming as well as diurnal and day-to-day fluctuations in temperature. Taken together, our results suggest that while temperature may play a role in regulating seed removal by ants, ant plant seed-dispersal mutualisms may be more robust to climate change than currently assumed

The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx)

1. Climate change is a world‐wide threat to biodiversity and ecosystem structure, functioning and services. To understand the underlying drivers and mechanisms, and to predict the consequences for nature and people, we urgently need better understanding of the direction and magnitude of climate change impacts across the soil–plant–atmosphere continuum. An increasing number of climate change studies are creating new opportunities for meaningful and high‐quality generalizations and improved process understanding. However, significant challenges exist related to data availability and/or compatibility across studies, compromising opportunities for data re‐use, synthesis and upscaling. Many of these challenges relate to a lack of an established ‘best practice’ for measuring key impacts and responses. This restrains our current understanding of complex processes and mechanisms in terrestrial ecosystems related to climate change. 2. To overcome these challenges, we collected best‐practice methods emerging from major ecological research networks and experiments, as synthesized by 115 experts from across a wide range of scientific disciplines. Our handbook contains guidance on the selection of response variables for different purposes, protocols for standardized measurements of 66 such response variables and advice on data management. Specifically, we recommend a minimum subset of variables that should be collected in all climate change studies to allow data re‐use and synthesis, and give guidance on additional variables critical for different types of synthesis and upscaling. The goal of this community effort is to facilitate awareness of the importance and broader application of standardized methods to promote data re‐use, availability, compatibility and transparency. We envision improved research practices that will increase returns on investments in individual research projects, facilitate second‐order research outputs and create opportunities for collaboration across scientific communities. Ultimately, this should significantly improve the quality and impact of the science, which is required to fulfil society's needs in a changing world

Evaluating the Influence of Disturbance and Climate on Red Spruce (Picea rubens Sarg.) Community Dynamics at its Southern Range Margin

Picea rubens(red spruce) populations experienced a synchronous rangewide decline in growth and vigor starting in the 1960’s, which was likely caused by climate change or environmental disturbances (e.g., acid deposition); However, it is yet unknown if populations continue to decline or have recovered. In the context of global warming, red spruce is a species of concern because it is at its southern continuous range margin in Massachusetts. This study uses tree-ring data coupled with population data from permanent plots to quantify the status of red spruce in Massachusetts. Tree cores were extracted from red spruce and used to examine radial growth rates, determine a growth-climate relationship, and document disturbance events. Red spruce at these plots ranged from 90 to 184 years old, and comprised 15 to 29 m2/ha-1 basal area. Over the past 50 years, red spruce has decreased in density, basal area, and relative importance while red maple, yellow birch, and American beech have increased. Red spruce saplings persisted in some plots, but the sapling layer was comprised mostly of American beech or red maple. However, red spruce seedlings were common at red spruce dominant plots indicating that if favorable conditions occur, it could return to its more dominant position in the canopy. Dendroclimatological analyses show that red spruce is sensitive to both temperature and precipitation. Most sites are correlated with temperature, while only twoforests were correlated to precipitation. The general temperature response of the red spruce studied was positively correlated with winter temperatures while the general precipitation response was negatively correlated with precipitation. Temporal analysis of the climate-growth response indicates that red spruce here have not had a temporally-stable, climate-growth relationship. Prior to 1960, radial growth was positively correlated with temperatures from November of the previous growing season to January of the current year. After 1960, all sites showed a shift in growth responses consistent with increased summer temperature stress; narrowed tree rings were formed during warm temperatures in July and August. Precipitation remained relatively constant over the past century, while temperatures have increased up to 2˚C across the study area. Of the two precipitation-sensitive forests, one forest shifted from being positively correlated with current January precipitation to negatively correlated with previous October precipitation while the second forest showed a strong positive relationship with August precipitation. Because the radial growth of red spruce here are mostly constrained by temperatures, there has been negative growth response to regional warming and precipitation has been stable, I suggest the change in climate response is potentially due to warming and a physiological threshold response to increasing temperatures. Interestingly, disturbance frequency and intensity have increased over the same time period, which could be either a trigger or a response to the shift in the growth-climate relationship

Seeing the forest for the trees: Tree species effects on soil microbial communities and nutrient cycling dynamics

Tree species influence soils above and belowground communities through leaf litter and root inputs. Soil microbial communities can directly influence tree growth and development through processes such as decomposition of leaves, and indirectly through chemical transformation of nutrients in soils as an influence of altered C:N ratios due to leaf litter and root inputs. This thesis aims to document some of the mechanisms by which trees influence soil microbial communities and nitrogen cycling processes like gross and net ammonification and nitrification. This thesis also aims to determine the role of site nitrogen status in modulating those tree species effects. The effects of tree species on ammonification and nitrification rates in forest floors and mineral soils were explored, and related to functional genetic markers for ammonia-oxidation by archaea and bacteria (amoA AOA and AOB), bacterial denitrification (nirS and nirK), and the general markers for bacteria (16S) and fungi (ITS). Two paired high-resolution laboratory methods were used to investigate the relationships between trees, soils, and the microbial communities, including molecular techniques such as quantitative polymerase chain reaction (qPCR) to target gene abundances in soils, and 15N pool-dilution experiments to understand how ammonium and nitrate are produced and consumed in soils. Soil samples were collected from two common garden experiments, named EP571 in Canada (Ribbons et al. 2016), and in Denmark, and both 15N and qPCR-based techniques were used to determine tree species effects and attribute N cycling processes to the abundances of functional genes. At EP571, western red cedar (Thuja plicata) forest floor nitrogen transformation rates differed from Douglas-fir (Pseudotsuga menziesii), Sitka spruce (Picea sitchensis), and western hemlock (Tsuga heterophylla), which corresponded with western red cedar having highest abundances of bacterial 16S and amoA AOA genes. A manipulative mesocosm (the Rhizotron) in Wales was used to determine how mixtures and monocultures of seedling species influenced tree growth, soil physical properties and soil microbial community structure and function within the first three years of growth. Within the Rhizotron experiment both alder (Alnus rubra) and Douglas-fir grew taller when grown in mixtures compared with monocultures of each species. Sycamore maple (Acer pseudoplatanus) acquired slightly greater aboveground biomass when planted in mixtures with common oak (Quercus robur), which attained less biomass in mixtures than monocultures. C:N ratios of leaves, stems, roots, and rhizospheric soils were determined to see if mixtures influenced C:N in trees. Rhizospheric soil microbial communities (including bacterial and fungal markers and the 4 genes tied to N cycling) were compared among the 4 tree species in the Rhizotron. Soil samples for microbial analyses were collected before seedlings were planted, and just before the experiment was harvested. These data show differences in height, biomass and C:N ratios between species can be observed at a seedling growth stage, but microbial communities may require longer exposure to develop. Lastly, the Bangor Diverse experiment was used to further explore diversity and mixture effects on soil microbial communities and N transformations. We found few mixture or monoculture tree species effects on mineral soil microbial communities or net nitrification or ammonification rates. Collectively, these stories shed light on the important functional role of soil microbes in forest soil N cycling. This thesis also highlights the use of isotope and microbial techniques for parsing out relationships between site, tree species identity and ecosystem functions, with the largest links observed between gross ammonification and microbial communities

Disturbance and climatic effects on red spruce community dynamics at its southern continuous range margin

Red spruce (Picea rubens) populations experienced a synchronous rangewide decline in growth and vigor starting in the 1960s, likely caused by climate change and a combination of environmental disturbances. However, it is not yet known if populations continue to decline or have recovered. Red spruce growing near its southern range margin in Massachusetts is a species of concern, in light of the vulnerability to climate change. This study uses population data from 17 permanent plots coupled with tree-ring data to examine radial growth rates, determine the growth-climate relationship, and document disturbance events. Red spruce at these plots ranged from 90 to 184 years old, and comprised 15 to 29 m2/ha basal area. Red spruce seedlings and saplings were common at plots with previously high overstory spruce abundance, indicating it could return to a more dominant position under favorable growing conditions. However, permanent plot measures over a 50 year time span did not indicate any consistent trends for changes in basal area or density for red spruce or other woody species. Climate data show that mean annual minimum, maximum, and summer temperatures have increased over the last 100 years. Dendroclimatological analyses indicated that red spruce growth was sensitive to both temperature and precipitation. Prior to the 1960s, spruce at these sites showed a positive response to precipitation; however after a multi-year drought in the 1960s showed an increasingly negative correlation with precipitation. There has been a negative growth response to regional warming, as spruce radial growth was mostly constrained by increasing temperatures, potentially coupled with the associated increasing drought-dress. I suggest the change in climate response is potentially due to a physiological threshold response to increasing temperatures, which may cause spruce to continue to decline or be lost from the lower elevation sites, while the high elevation sites has a persistent spruce population