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.

Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.

The mechanisms underlying community composition and diversity of soil archaea are poorly understood. We compared both total archaea and ammonia oxidizing archaea (AOA) using 16S rRNA and amoA genes pyrosequencing respectively, in two different biomes: tropics (Malaysia), and temperate (Korea and Japan). Despite differences in characteristics of these biomes, we found that at the broad taxonomic level the dominant archaeal lineages are the same, except in certain instances (16S rRNA gene: group 1.1a Thaumarchaeota; amoA gene: Nitrososphaera and Nitrosotalea lineages). However, at the OTU level, both total archaea and AOA communities showed biome-specific patterns, indicating that at lower taxonomic levels biome differences are also important. In both biomes, total archaeal diversity showed a negative correlation with pH, but a hump-shaped curve for AOA diversity, peaking at ∼pH 6.0. Within each biome, pH also emerged as the delimiting factor determining variation in community composition of both total archaea and AOA. Communities from each biome clustered separately, even at analogous pH levels. At the OTU level, certain shared OTUs did occur at approximately the same pH range in both biomes. We found that closely related OTUs of both total archaea and AOA respectively tended to co-occur, suggesting that in evolutionary terms these closely related lineages have conserved very similar ecological requirements. This predictability also strongly suggests that soil archaeal community assembly has strongly deterministic aspect. Overall, our findings emphasize that soil archaeal communities are to large extent predictable and structured by both biome and by soil chemical environment, especially pH.

were measured at the photosynthetic steady state at least 10 The effects of strong light in combination with elevated tempermin after the light exposure (180 mmol m − 2 s − 1 PFD). Stable atures on the photosynthetic system were examined in 4 dipterocarp tree species with ecologically different habitats. temperature responses of DF/F% m and q P were observed in S. The 4 dipterocarp tree species were: Shorea platyclados origi-platyclados and D. oblongifolius, while those in S. par7ifolia and S. assamica were more temperature-dependent and severely nated from upper dipterocarp forests, Shorea par7ifoliaaffected at 45°C. Little difference was observed in temperature-lowland and hill dipterocarp forests, Shorea assamica -lowland dipterocarp forests, and Dipterocarpus oblongifolius -dependent F% v /F% m among species. Photoinhibitory light exposure riparian fringes. S. platyclados and D. oblongifolius have (1600 mmol m − 2 s − 1 PFD) for 2 h at 40°C had little effect on higher growth and survival rates in open sites than S. par7ifolia the recovery kinetics from photoinhibition of S. platyclados and D. oblongifolius compared with those at 35°C. In contrast, the and S. assamica. Tolerance of high temperature among the recovery from photoinhibition was retarded in S. par7ifolia and species was assessed by determining the critical temperatures (T c ) at which the minimal fluorescence (F o ) began to rise S. assamica. These findings suggest that even at 40°C, a sharply. This was measured by exposing plants to an increasing temperature below T c , an exposure to strong light exacerbated photoinhibition in S. par7ifolia and S. assamica corresponding temperature of about 1°C min − 1 . The intrinsic thermotolerto the closure of PSII reaction centers, as indicated by the ance of the thylakoid membrane appears to be the highest for decrease in q P at this temperature. Thus, S. platyclados and D. D. oblongifolius (T c =46.4°C), intermediate for S. platyclados (45.7°C), and lowest for S. par7ifolia and S. assamica (45.2 and oblongifolius, which occur at uplands and riparian fringes with 45.3°C, respectively). The temperature-dependent efficiency of frequent disturbances, are suggested to have higher photosynthetic tolerance to elevated temperatures contributing to a PSII electron transport (DF/F% m ), photochemical quenching circumvention of photoinhibition. (q P ), and the efficiency of light capture of open PSII (F% v /F% m )