Browsing by Author "Kerfahi, Dorsaf"
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Item Open Access Distinctive soil archaeal communities in different variants of tropical equatorial forest(Springer, 2017-11-29) Kerfahi, Dorsaf; Tripathi, Binu M.; Ferry Slik, J. W.; Sukri, Rahayu S.; Jaafar, Salwana; Adams, Jonathan M.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.Item Open Access From the high Arctic to the equator: do soil metagenomes differ according to our expectations(Springer, 2018-06-07) Kerfahi, Dorsaf; Tripathi, Binu M.; Dong, Ke; Kim, Mincheol; Kim, Hyoki; Ferry Slik, J. W.; Go, Rusea; Adams, Jonathan M.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.Item Open Access Soil nematodes show a midelevation diversity maximum and elevational zonation on Mt. Norikura, Japan(Nature Publishing Group, 2017-06-08) Dong, Ke; Moroenyane, Itumeleng; Tripathi, Binu; Kerfahi, Dorsaf; Takahashi, Koichi; Yamamoto, Naomichi; An, Choa; Cho, Hyunjun; Adams, JonathanLittle 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.Item Open Access Temperature effects on the first three years of soil ecosystem development on volcanic ash(Elsevier, 2018-08-13) Tateno, Ryunosuke; Tatsumi, Chikae; Nakayama, Masataka; Takahashi, Koichi; Kerfahi, Dorsaf; Adams, JonathanLittle 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.