Rainforest conversion to rubber plantation may not result in lower soil diversity of bacteria, fungi, and nematodes

Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function

The Impact of Selective-Logging and Forest Clearance for Oil Palm on Fungal Communities in Borneo

Tropical forests are being rapidly altered by logging, and cleared for agriculture. Understanding the effects of these land use changes on soil fungi, which play vital roles in the soil ecosystem functioning and services, is a major conservation frontier. Using 454-pyrosequencing of the ITS1 region of extracted soil DNA, we compared communities of soil fungi between unlogged, once-logged, and twice-logged rainforest, and areas cleared for oil palm, in Sabah, Malaysia. Overall fungal community composition differed significantly between forest and oil palm plantation. The OTU richness and Chao 1 were higher in forest, compared to oil palm plantation. As a proportion of total reads, Basidiomycota were more abundant in forest soil, compared to oil palm plantation soil. The turnover of fungal OTUs across space, true β-diversity, was also higher in forest than oil palm plantation. Ectomycorrhizal (EcM) fungal abundance was significantly different between land uses, with highest relative abundance (out of total fungal reads) observed in unlogged forest soil, lower abundance in logged forest, and lowest in oil palm. In their entirety, these results indicate a pervasive effect of conversion to oil palm on fungal community structure. Such wholesale changes in fungal communities might impact the long-term sustainability of oil palm agriculture. Logging also has more subtle long term effects, on relative abundance of EcM fungi, which might affect tree recruitment and nutrient cycling. However, in general the logged forest retains most of the diversity and community composition of unlogged forest

Temperature effects on the first three years of soil ecosystem development on volcanic ash

Little is known of the earliest stages of soil ecosystem development on volcanic ash, and how this process is affected by temperature. We studied the first three years of soil development in a field-based mesocosm experiment, situated in different climates across Japan. Newly fallen, sterilized volcanic ash from the Sakurajima volcano (Kyushu, Japan) was placed into pots and positioned at six locations with mean annual temperatures ranging from - 1.6 °C to 18.6 °C. At 24 months into the experiment, C and N accumulation showed only a weak linear correlation with temperature, but by 36 months there was a clear exponential relationship. This applied only to the top 2 cm of the developing soil, and was not apparent in the lower part of the ash. We suggest that this acceleration in warmer climates relates to a positive feedback involving bryophyte cover, which had become much denser by the third year in the warmer sites. Surprisingly, the abundance of 16S rRNA gene copies of bacteria, fungi, archaea - as well as ammonia oxidizers – did not increase from 12 months to 36 months, and did not show any relationship to temperature, suggesting that input from plants is the major factor in increasing C and N buildup in the soil. Overall it appears that temperature effects on bryophyte cover buildup may be important in controlling the temperature relationship in soil development on volcanic ash

Do tropical rain forest soils have greater nematode diversity than high arctic tundra? a metagenetic comparison of Malaysia and Svalbard

Aim Latitudinal differences in diversity have long fascinated ecologists. It is unclear whether small soil animals such as nematodes show latitudinal differences in diversity. Based on hypotheses concerning the basis for greater tropical diversity, and by analogy with other groups, we predicted (1) greater alpha diversity in the equatorial tropics than the High Arctic, (2) greater beta and gamma diversity in the tropics. We also predicted (3) no species overlap between the tropics and the High Arctic, and (4) lower abundance of root feeding and insect parasitic nematodes in the high Arctic. Location We sampled at three sites in equatorial rain forest in Malaysia at 2° N and three sites in High Arctic tundra in Svalbard at 79° N. Methods In Malaysia and Svalbard, three sets of 1-m2 samples were taken, in interrupted grids. Nematodes were extracted using a Baermann funnel. Bulk DNA was amplified by polymerase chain reaction for the 18S rRNA gene, followed by 454-pyrosequencing. Results Comparing operational taxonomic unit (OTU)-based nematode communities (99% sequence similarity), averaged alpha diversity per 1-m2 quadrat showed no difference between Malaysia and Svalbard. However, the classic beta diversity and gamma diversity of nematodes was higher for Malaysia. Main conclusions There was, surprisingly, no difference in the alpha diversity of nematodes between Malaysia and Svalbard. However, for beta and gamma diversity, diversity was higher in Malaysia. There was also considerable OTU overlap between the two regions, suggesting that very broad climatic niches are common in nematode ecology. Plant root feeders and insect parasites were relatively more common in Svalbard. Overall, we found a mixed and complex picture in terms of agreement with what would be predicted on the basis of ecological theory and observations on other groups. While further confirmatory studies would be beneficial, there is a need to incorporate these new findings in the formulation of hypotheses and tests for the underlying causes of latitudinal trends

Distinctive soil archaeal communities in different variants of tropical equatorial forest

Little is known of how soil archaeal community composition and diversity differ between local variants of tropical rainforests. We hypothesized that (1) as with plants, animals, fungi, and bacteria, the soil archaeal community would differ between different variants of tropical forest; (2) that spatially rarer forest variants would have a less diverse archaeal community than common ones; (3) that a history of forest disturbance would decrease archaeal alpha- and beta-diversity; and (4) that archaeal distributions within the forest would be governed more by deterministic than stochastic factors. We sampled soil across several different forest types within Brunei, Northwest Borneo. Soil DNA was extracted, and the 16S rRNA gene of archaea was sequenced using Illumina MiSeq. We found that (1) as hypothesized, there are distinct archaeal communities for each forest type, and community composition significantly correlates with soil parameters including pH, organic matter, and available phosphorous. (2) As hypothesized, the “rare” white sand forest variants kerangas and inland heath had lower archaeal diversity. A nestedness analysis showed that archaeal community in inland heath and kerangas was mainly a less diverse subset of that in dipterocarp forests. However, primary dipterocarp forest had the lowest beta-diversity among the other tropical forest types. (3) Also, as predicted, forest disturbance resulted in lower archaeal alpha-diversity—but increased beta-diversity in contrast with our predictions. (4) Contrary to our predictions, the BetaNTI of the various primary forest types indicated community assembly was mainly stochastic. The possible effects of these habitat and disturbance-related effects on N cycling should be investigated

Soil nematodes show a midelevation diversity maximum and elevational zonation on Mt. Norikura, Japan

Little is known about how nematode ecology differs across elevational gradients. We investigated the soil nematode community along a ~2,200 m elevational range on Mt. Norikura, Japan, by sequencing the 18S rRNA gene. As with many other groups of organisms, nematode diversity showed a high correlation with elevation, and a maximum in mid-elevations. While elevation itself, in the context of the mid domain effect, could predict the observed unimodal pattern of soil nematode communities along the elevational gradient, mean annual temperature and soil total nitrogen concentration were the best predictors of diversity. We also found nematode community composition showed strong elevational zonation, indicating that a high degree of ecological specialization that may exist in nematodes in relation to elevation-related environmental gradients and certain nematode OTUs had ranges extending across all elevations, and these generalized OTUs made up a greater proportion of the community at high elevations – such that high elevation nematode OTUs had broader elevational ranges on average, providing an example consistent to Rapoport’s elevational hypothesis. This study reveals the potential for using sequencing methods to investigate elevational gradients of small soil organisms, providing a method for rapid investigation of patterns without specialized knowledge in taxonomic identification

From the high Arctic to the equator: do soil metagenomes differ according to our expectations

Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon “classical” views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them

Responses of Intertidal Bacterial Biofilm Communities to Increasing pCO2

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Land use not litter quality is a stronger driver of decomposition in hyperdiverse tropical forest

Funded by Natural Environment Research Council. Grant Number: NE/K016253/1Peer reviewedPublisher PD