Bacteria play important roles in the transformation of nutrients in wetlands, but few studies have examined parameters affecting variation in bacterial community composition between wetlands. We compared the composition of eubacterial and denitrifying bacterial biofilm communities in 32 agricultural constructed wetlands in southern Sweden, and the extent to which wetland environmental parameters could explain the observed variation. Structure and richness of the eubacterial 16S rRNA gene and three denitrifying bacterial enzyme genes (nirK, nirS and nosZ), analysed by molecular fingerprinting methods, varied among the constructed wetlands, which could be partly explained by different environmental parameters. Results from the enzyme gene analyses were also compared to determine whether the practice of using a single denitrifying bacterial gene could characterize the overall community composition of denitrifying bacteria. We found that nirK was more diverse than both nirS and the nosZ, and the band structure and richness of the three genes were not related to the sam environmental parameters. This suggests that using a single enzyme gene may not suffice to characterize the community composition of denitrifying bacteria in constructed agricultural wetlands. / <p>Included in doctoral thesis: Milenkovski, Susann. Structure and Function of Microbial Communities in Constructed Wetlands - Influence of environmental parameters and pesticides on denitrifying bacteria. Lund University 2009.</p>

In the Central Valley of Costa Rica in the Department of Heredia, I investigated the soil chemical properties and microbial communities under four native shade tree species in a coffee agroforestry system. In the second year of the study, Effective Microorganisms, a microbial inoculant, was applied to examine its effect on soil chemistry. The shade tree species included in this study were Anonna muricata L., Diphysa americana Mill., Persea americana Mill., and Quercus spp. L. Plots measured 20 by 30 meters and were replicated three times for each shade tree species except for Quercus spp., which only had two replications. Twelve composite soil samples were collected from each plot in 2008 and again in 2009, and twelve composite foliar samples were taken from the coffee plants in each plot in 2008. The results of this study indicated that the species of native shade tree had a significant effect on soil ammonium-N, nitrate-N, total dissolved nitrogen and magnesium. Sun or shade position had a significant effect on dissolved organic nitrogen and dissolved organic carbon. The species of native shade tree also had a significant effect on the composition of soil microbial communities. PLFA analysis revealed a significant difference in soil fungi abundance in soil samples from Annona plots relative to those from Persea plots. Effective microorganisms in combination with the tree species, as well as in combination with species and sun or shade position, had a significant interaction effect on soil ammonium-N, with the EM-treated plots showing higher concentrations of soil ammonium-N. There was a significant positive correlation between soil pH and foliar calcium, as well as soil dissolved organic nitrogen and foliar %N, at p< 0.01. This study suggests that Quercus spp. is a tree species that may help to regulate the cycling of nitrogen in the coffee agroecosystem. Annona muricata appears to inhibit the action of some fungal species and may reduce the occurrence of fungal pathogens in the soil, although the present study did not explore this issue. Although Diphysa americana is a legume, it does not appear to increase the amount of soil nitrogen in the vicinity of the coffee plants themselves. All four tree species in this study improve coffee soils by increasing soil concentrations of dissolved organic nitrogen and dissolved organic carbon. Coffee yield data and long term observations on the health of the coffee plants would clarify whether one of these species is particularly beneficial, from an agronomic perspective, for the productivity of this coffee agroecosystem.

No description available.

A study of the aquatic invertebrate communities from two locations (Location 1 and Location 2) within the Matapouri catchment in Northland, New Zealand, was conducted to assess community structure in differing local-scale habitats. Four data collection methods were utilised generating 33,058 adult or larval invertebrates. The sampling methods comprised benthic kick-sampling, sticky trapping, light trapping, and emergence trapping. For the sticky trapping and light trapping, sampling was carried out at three different sites (Sites 1–3) within each location. The sites were situated within three habitat types; native forest, native forest-fringe, and raupo wetland. Emergence trapping also commenced within the three sites, at both locations, but was discontinued after two months, due to the equipment being destroyed by consecutive flooding events (method described in Appendix 1). Benthic sampling was carried out within the Forest and Forest-fringe habitats. Benthic sampling, sticky trapping, and light trapping were carried out following a monthly schedule between June and November 2005. Conductivity, pH, and water temperature measurements were taken concurrently with benthic sampling on a monthly basis, while water velocity and substrate measurements were taken once to assist in habitat characterisation. Overall, 71 taxa were recorded by benthic sampling over the six month period, with a mean of approximately 30 taxa per site per month. In comparison with similar studies elsewhere in New Zealand, a figure of around 30 taxa per sample was high. The benthic macroinvertebrate fauna at all sites was dominated by Trichoptera (19 taxa), Diptera (16 taxa) and Ephemeroptera (10 taxa). This pattern of diversity is similar to that reported in other New Zealand studies. However, in contrast to previous studies, the leptophlebiid mayfly genus Deleatidium was not numerically dominant over the rest of the community, and other leptophlebiid genera (Acanthophlebia, Atalophlebioides, Mauiulus and Zephlebia) were equally represented, possibly reflecting niche partitioning between the groups. The genus Nesameletus was not recorded at any site, despite being one of the core mayfly species in New Zealand streams. The rare mayfly Isothraulus abditus was recorded at one of the forest locations. There are no published records of this species from Northland. Although acknowledged as another of the core New Zealand benthic taxa, the hydropsychid caddisfly Aoteapsyche was not recorded during the study. However, another hydropsychid, Orthopsyche, was commonly recorded, and these may be filling a similar niche to the Aoteapsyche genus. In contrast to the Trichoptera, Diptera, and Ephemeroptera, the Plecoptera fauna was relatively depauperate, probably reflecting the warmer climate of the region and lack of temperature-buffered spring-fed streams. Surprisingly, Zelandobius, a core New Zealand genus, was absent but is regularly recorded in Northland. A species of conservation interest, Spaniocercoides watti, currently recognised as a Northland endemic, was recorded in low numbers. There were no apparent trends in diversity or abundance of benthic invertebrates over time. Also, there were no significant differences in species diversity between the two locations. However, in many cases, taxa were more abundant at Location 2. This may have been due to steeper gradients at Location 2, and the consequent effects on substrate size and streambed stability, as all other physical factors appeared similar between locations. Although several significant differences of individual benthic taxa were recorded, no broad effect of habitat (sites) on species diversity was observable. However, at Location 2, abundances were significantly higher at Site 3 (Forest) compared to Site 2 (Forest-fringe). The reasons were uncertain, but may be attributed to higher retention of allochthonous organic materials, trapped by in-stream cover and larger substrates. Investigations of adult stages by sticky traps supported benthic results recording community compositions and abundances dominated by Trichoptera and Diptera. Plecoptera were poorly represented. Location 2 recorded higher abundances of taxa, particularly Ephemeroptera and Plecoptera. Investigations of adult stages by light traps however did not produce any statistically significant differences in abundances between sites, between locations, or between sites across locations, and it is believed to be due to limited sampling replication combined with some biases of light trapping. This study indicates that the aquatic invertebrate community at Matapouri is diverse but also reasonably representative. Several rare or uncommon insects inhabit the catchment. It is therefore important that Iwi and the local Landcare Group, who invited and supported this research, together with the Department of Conservation, continue their efforts in protecting these areas. The resident fauna have the capacity to restock areas downstream, which are intended to be improved and restored through sediment control and riparian management.

A study of the aquatic invertebrate communities from two locations (Location 1 and Location 2) within the Matapouri catchment in Northland, New Zealand, was conducted to assess community structure in differing local-scale habitats. Four data collection methods were utilised generating 33,058 adult or larval invertebrates. The sampling methods comprised benthic kick-sampling, sticky trapping, light trapping, and emergence trapping. For the sticky trapping and light trapping, sampling was carried out at three different sites (Sites 1–3) within each location. The sites were situated within three habitat types; native forest, native forest-fringe, and raupo wetland. Emergence trapping also commenced within the three sites, at both locations, but was discontinued after two months, due to the equipment being destroyed by consecutive flooding events (method described in Appendix 1). Benthic sampling was carried out within the Forest and Forest-fringe habitats. Benthic sampling, sticky trapping, and light trapping were carried out following a monthly schedule between June and November 2005. Conductivity, pH, and water temperature measurements were taken concurrently with benthic sampling on a monthly basis, while water velocity and substrate measurements were taken once to assist in habitat characterisation. Overall, 71 taxa were recorded by benthic sampling over the six month period, with a mean of approximately 30 taxa per site per month. In comparison with similar studies elsewhere in New Zealand, a figure of around 30 taxa per sample was high. The benthic macroinvertebrate fauna at all sites was dominated by Trichoptera (19 taxa), Diptera (16 taxa) and Ephemeroptera (10 taxa). This pattern of diversity is similar to that reported in other New Zealand studies. However, in contrast to previous studies, the leptophlebiid mayfly genus Deleatidium was not numerically dominant over the rest of the community, and other leptophlebiid genera (Acanthophlebia, Atalophlebioides, Mauiulus and Zephlebia) were equally represented, possibly reflecting niche partitioning between the groups. The genus Nesameletus was not recorded at any site, despite being one of the core mayfly species in New Zealand streams. The rare mayfly Isothraulus abditus was recorded at one of the forest locations. There are no published records of this species from Northland. Although acknowledged as another of the core New Zealand benthic taxa, the hydropsychid caddisfly Aoteapsyche was not recorded during the study. However, another hydropsychid, Orthopsyche, was commonly recorded, and these may be filling a similar niche to the Aoteapsyche genus. In contrast to the Trichoptera, Diptera, and Ephemeroptera, the Plecoptera fauna was relatively depauperate, probably reflecting the warmer climate of the region and lack of temperature-buffered spring-fed streams. Surprisingly, Zelandobius, a core New Zealand genus, was absent but is regularly recorded in Northland. A species of conservation interest, Spaniocercoides watti, currently recognised as a Northland endemic, was recorded in low numbers. There were no apparent trends in diversity or abundance of benthic invertebrates over time. Also, there were no significant differences in species diversity between the two locations. However, in many cases, taxa were more abundant at Location 2. This may have been due to steeper gradients at Location 2, and the consequent effects on substrate size and streambed stability, as all other physical factors appeared similar between locations. Although several significant differences of individual benthic taxa were recorded, no broad effect of habitat (sites) on species diversity was observable. However, at Location 2, abundances were significantly higher at Site 3 (Forest) compared to Site 2 (Forest-fringe). The reasons were uncertain, but may be attributed to higher retention of allochthonous organic materials, trapped by in-stream cover and larger substrates. Investigations of adult stages by sticky traps supported benthic results recording community compositions and abundances dominated by Trichoptera and Diptera. Plecoptera were poorly represented. Location 2 recorded higher abundances of taxa, particularly Ephemeroptera and Plecoptera. Investigations of adult stages by light traps however did not produce any statistically significant differences in abundances between sites, between locations, or between sites across locations, and it is believed to be due to limited sampling replication combined with some biases of light trapping. This study indicates that the aquatic invertebrate community at Matapouri is diverse but also reasonably representative. Several rare or uncommon insects inhabit the catchment. It is therefore important that Iwi and the local Landcare Group, who invited and supported this research, together with the Department of Conservation, continue their efforts in protecting these areas. The resident fauna have the capacity to restock areas downstream, which are intended to be improved and restored through sediment control and riparian management.

Proper management of soil organic matter (SOM) contributes to increasing plant productivity and reducing dependency on mineral fertilizers. Organic matter is widely regarded as a vital component of a healthy soil as it plays an important role in soil physical, chemical and biological fertility. Plant residues are the primary source of SOM. Therefore, proper SOM management requires a better understanding of plant residue decomposition kinetics in order to synchronize nutrient release during decomposition and plant uptake and prevent nutrient losses. In natural and managed ecosystems, residues are added frequently to soil, in the form of dead roots and litter fall of plant species with different C/N ratios. However, in most studies on residue decomposition, residues with different C/N ratios are added once and the effect of the presence of plants on residue decomposition is rarely investigated. In this project, four experiments were carried out with different objectives in order to close these knowledge gaps. The aim of the first experiment was to investigate the effect of frequent wheat residue addition on C mineralization and N dynamics. The experiment consisted of five treatments with different frequency of residue addition (2% w/w of wheat residues in total): once (100%W), every 16 days (25%), every 8 days (12.5%) or every 4 days (6.25%) and noresidue addition (control) with four replicates. The results showed that increasing frequency of low-N wheat residue addition increased C mineralization. Compared to 100%W, cumulative respiration per g residue at the end of the incubation (day 80) was increased by 57, 82 and 92% at 25%W, 12.5%W and 6.25%W, respectively. Despite large increases in cumulative respiration, frequent residue addition did not affect inorganic N or available N concentrations, microbial biomass C and N or soil pH. It is concluded that experiments with single residue additions may underestimate residue decomposition rates in the field because with several additions, soil microbes respire more of the added C (and possibly native soil C) per unit biomass but that this does not change their N requirements or the microbial community composition. In the second experiment, the effect of mixing of high and low C/N residues at different times during incubation was investigated. There were 4 addition times; 25% of a total of 2% (w/w) residue was added either as wheat (high C/N) or lupin (low C/N) residue. Wheat residue was added to lupin residues on days 16 (LW-16), 32 (LW-32) or 48 (LW-48). Additional treatments were 100%L (added 25% of lupin residues on days 0, 16, 32 and 48) and 100%W (added 25% of wheat residues on days 0, 16, 32 and 48) and 0% (the control) with four replicates. Adding high C/N residues into decomposing low C/N ratio residue strongly decreased the respiration rate compared to the addition of low C/N residues, and lowered the availability of inorganic N, but significantly increased soil pH and altered microbial community composition. By the end of the incubation on day 64, the cumulative respiration of LW-16, LW-32 and LW-48 was similar and approximately 30% lower than in the treatment with only lupin residue addition. The third experiment studied the effect of spatial separation of high and low C/N residues on decomposition and N mineralization. Each microcosm consisted of two PVC caps of 70 mm diameter and 20 mm height with the open end facing each other separated by a 30μm mesh. The caps were filled with soil mixed with either low or high C/N residue with three replicates. Contact of high and low C/N residues led to an increase in the decomposition rate of the high C/N residues at the interface whereas it decreased it in the low C/N residues. The results showed that N and soluble C compounds moved from the easily decomposable residues into the surrounding soil, thereby enhancing microbial activity, increasing inorganic N and significantly changing soil pH in the layer 0-5 mm from the interface compared to the 5-10 mm layer of the high C/N residues, whereas the movement of soluble C and N to high C/N residues decreased the decomposition of the low C/N residues. The final experiment investigated the effect of living plants on decomposition of high and low C/N residues. Wheat was grown in pots with a 30 μm mesh at the bottom. After a root mat had formed (>50% root coverage), a PVC cap with soil with high and low C/N residues (2% w/w) was placed against the mesh. The presence of plant roots significantly increased the respiration rate, N immobilization and increased the soil pH in the 0-5 mm layer in the first 4 days compared to the 5-10 mm layer. This enhanced microbial activity (and probably microbial biomass) can be explained by root exudates. The microbial community composition of plant treatments differed significantly from treatments without plants and the effect was greater in the immediate vicinity of the roots. / Thesis (M.Ag.Sc.) -- University of Adelaide, School of Earth and Environmental Sciences, 2009

Swamp-breeding treefrogs form conspicuous components of many tropical forest sites, yet remain largely understudied. The La Selva Biological Station, a rainforest reserve in Costa Rica, harbors a rich swamp-breeding treefrog fauna that has been studied in only one of the many swamps found at the site. To understand if the species composition of treefrogs at La Selva varies over space or time, frogs were censused in 1982-83, 1994-95, 2005 and 2011 at two ponds located in the reserve. Data on treefrog habitat utilization were also collected. Species composition varied spatially only in 2011. Temporal variation was observed at both ponds for all groups tested. Habitat use varied among species and between swamps. The pattern of variation suggests that temporally dynamic systems such as temporary Neotropical forest swamps will converge and diverge in species composition over time.

No description available.

In the Boreal region, the length of day and night varies extremely over the year and organisms are exposed to different diel (24 h) fluctuations of light and temperature. Among them are pelagic populations of bacteria that are ubiquitous in freshwater ecosystems. The structure of prokaryotic assemblages in lakes is regulated by both abiotic and biotic parameters known to have diel patterns; yet, knowledge on changes of the active bacterial community composition (aBCC) over diel cycles is limited, especially at short temporal scales. Here, measurements of physicochemical parameters, nutrient levels and chlorophyll a concentrations, characterization of the carbon pool and 16S rRNA sequencing were used to elucidate the aBCC in a peat bog and the oligotrophic lake Klocka in Jämtland county, Sweden. I show that the activity of bacterioplankton communities remained relatively stable at 6-h intervals and did not follow any diel patterns during an uneven light regime period in June. However, the activity of peat bog communities changed in a cyclic pattern over three diel cycles during an even light period in September, whereas diel changes did not substantially differentiate between sampling periods and among depths in Klocka. The results of the thesis provide valuable insights into the importance of diel cycles in bacterial diversity and community dynamics in lentic habitats.

A large database now exists for tardigrades in the Great Smoky Mountains National Park (GSMNP) consisting of 780 samples, 15,618 specimens, and 80 species including 14 new to science. We found 43 species of tardigrades in 150 soil/leaf litter samples. We calculated the Chao 1 species richness estimate with the species accumulation curve for the GSMNP and confirmed that our species list is virtually complete. Compared with soil data from mt. Fuji, Japan, estimated species richness in GSMNP was significantly higher. In our comparison of previous studies of soil/leaf litter tardigrades in other geographic areas, only the Kanagawa prefecture of Japan reported a higher number of species (47) than the GSMNP. Species richness estimators are valuable tools for comparing diversity in different habitats, even when sampling effort varies between studies.