The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.

Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.

The fossil record suggests greater diversity of insect leaf feeding during warm climate intervals. Much published work in the paleobotanical literature has been based on the presumed validity of this pattern. However, the existence of this pattern in nature has never been tested from the present-day world. Here we ask, is it true that on average, in warmer climates, a leaf is being eaten in more ways? We compared forests at seven sites in northern Florida (30° N, MAT ca. 19.5 °C) to seven sites across the northeastern USA (40-42° N, MAT 7-9 °C). Presence and absence of damage types were determined using a standard leaf damage guide; 93 damage types were found in the Florida samples and 80 in the northeastern samples. In bulk floras, there was a consistent difference in damage diversity, on a per-leaf basis (as in the fossil studies), between Florida and northeastern sites. Florida sites had a greater number of damage types. When northern and southern populations of individual tree species were compared, higher southern damage diversity was found in four species (Acer rubrum, Acer saccharum, Fagus grandifolia, and Quercus coccinea), though with no difference with latitude in a fifth species (Quercus alba). These results appear to validate that the trend seen in the fossil record is not a spurious effect of site differences. They also extend a pattern seen in deep time into the present day, adding greatly to its generality.

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Environmental abiotic and biotic factors are important in controlling soil CO2 efflux in forest ecosystems of different ages, as they play an important role in soil respiration. In understanding the spatial and temporal variation of soil CO2 efflux after several years of forest logging, there is a need to quantify the changing soil properties, environmental factors, and the total above and below ground biomass. This study was conducted in a 50-year old recovering tropical lowland forest in Peninsular Malaysia, measuring soil CO2 efflux using the continuous open flow chambers technique connected to a multi gas-handling unit and infrared gas analyser. The aim of this study was to determine the spatial and temporal variation of soil CO2 efflux in relation to changes in soil properties, environmental factors and forest carbon in a recovering forest. The efflux rates of about 389.20, 634.78, 564.81, 537.92 and 428.72 mg m−2 h−1, respectively, varied across the days and months, increasing from February and attaining the maximum in March and then gradually decreasing from April to June. The soil properties revealed a considerable amount of soil organic carbon, total organic carbon, and soil organic carbon stock, while the total above ground biomass, below ground biomass, soil pH, nitrogen to carbon ratio were found to provide nutrients for microbial activities in soil and to emit soil CO2. The multiple linear regression model indicated that the soil temperature and moisture explained the spatial and temporal variation in soil CO2 efflux; likewise, the changes in the soil properties and forest carbon significantly increased the soil CO2 efflux indicating a strong positive correlation (R 2 = 0.93).