The impact of tropical forest logging and oil palm agriculture on the soil microbiome

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land‐use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once‐logged and twice‐logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell–cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land‐use changes on the interaction of soil microbes.     

The impact of forest continuity and management on forest floor vegetation evaluated by species traits

The distribution of the flora with different species attributes are investigated in two studies of forest ecosystems in Denmark, One study compared 17 forests with different degrees of management, the other study compared the flora of 25 old forests with that of 6 new forests. No effect of forest management could be detected in the distribution of species attributes in the flora, whereas the forest continuity was correlated with almost all of the 14 traits investigated. Species with heavy seeds, transient seedbanks, ant dispersed seeds, early and short flowering time, low stature and high extent of lateral spread were more common in old forests, while the proportion of species with small, short-lived seeds, epizoochorous dispersal, little lateral spread and later and longer flowering period was higher in new forests. In particular, Raunkiaers therophyles, and ruderal species were more common in new forests than in old.
Differences in the effects of the two types of disturbance - forest management, and breaks in forest eontinuity - are discussed in relation to survival strategies of the forest flora. The importanee of persistence ability in contrast to colonisation ability is stressed for many forest plants.     

The impact of selective logging on forest structure and tenrec populations in western Madagascar

Summary This paper reports on possible effects of selective logging on vegetation structure and its consequences for two tenrec species in a dry forest in western Madagascar. On a small scale semi-mechanized logging of less than 10 m³ per ha alters forest structure significantly. However on a large scale most of these changes are smaller than the variation of forest structure due to natural causes. The most profound ecological effect of logging is a reduction in the number of woody species in the regenerating cohort of trees. Potential longterm consequences of this feature are discussed. Microhabitat variables influencing the habitat utilization of two tenrec species,Echinops telfairi andTenrec ecaudatus, were identified in an area of unlogged forest. The conclusions derived from this analysis were then tested in other parts of the forest which had been modified by selective logging. Logging of the extent described above slightly impairs habitats forE. telfairi but has no effect onT. ecaudatus. Though the latter species is hunted extensively in the logged areas, loggingper se does not threaten the survival of either species.

---

Résumé Cette étude met en évidence quelques effets de l'exploitation séléctive de la forêt sur la structure de la végétation et les conséquences pour deux espèces de tenrecs dans une forêt sèche à l'ouest de Madagascar. Dans un domaine limité, l'exploitation de bois de moins de 10 m³ par ha change considérablement la structure de la forêt. Mais si on considère une échelle plus grande, ces effets sont inférieurs à la variabilité naturelle. L'effet le plus grave de l'exploitation forestière sélective est la reduction du nombre d'espèces végétales ligneuses dans le processus de regénération naturelle de la forêt. Quelques conséquences possibles de cette réduction pour les animaux sont discutées. Quelques caractères distinctifs de la végétation qui influencent l'utilisation de l'habitat par deux espèces de tenrec,Echinops telfairi etTenrec ecaudatus, ont été identifiés dans une partie de la forêt qui n'a pas encore été exploitée. Les conclusions de cette analyse sont vérifiées dans une autre partie de la forêt qui a été modifiée par l'exploitation du bois. L'exploitation forestière sélective du bois détériore légèrement l'habitat pourE. telfairi, mais elle n'a pas d'effets remarquables surT. ecaudatus. L'exploitation sélective du bois favorise la chasse par l'ouverture de chemins d'accès. La chasse deT. ecaudatus est particulièrement intense, mais cependant ni l'une ni l'autre des espèces de tenrec considérées ne sont en danger d'extinction par cette form d'exploitationper se.

     

Controls on leaching from coniferous forest floor microcosms

Summary Studies were conducted with coniferous forest floor microcosms to examine the potential influence of acid precipitation, temperature changes, and plant uptake upon the chemistry of soil leachate solutions. The experimental design included two temperatures and three different simulated throughfall chemistry treatments. When the acidity of throughfall inputs to the microscosms increased, the forest floors exhibited increased leaching losses of calcium, magensium, potassium, and ammonium. The fact that aluminum losses did not incrase correspondingly suggested that there may be a kinetic lag in the mobilization and leaching of aluminum. When microcosms were exposed to warmer temperatures, percolates showed increased leaching losses of calcium, potassium, ammonium, sulfate, nitrate, and organic anions. Forest floor microcosms exposed to simulated average field conditions behaved very much like field plots under the same environmental conditions; however, there were predictable differences in leaching losses between laboratory and field systems for those ions which are strongly controlled by plant uptake. In general, the exclusion of plant uptake from microcosms resulted in increased leaching of potassium, nitrate, ammonium. and sulfate relative to field plots.     

A survey of indigenous microbial hydrocarbon degradation genes in soils from Antarctica and Brazil

Total community DNA from 29 noncontaminated soils and soils impacted by petroleum hydrocarbons and chloro-organics from Antarctica and Brazil were screened for the presence of nine catabolic genes, encoding alkane monooxygenase or aromatic dioxygenases, from known bacterial biodegradation pathways. Specific primers and probes targeting alkane monooxygenase genes were derived from Pseudomonas putida ATCC 29347 (Pp alkB), Rhodococcus sp. strain Q15 (Rh alkB1, Rh alkB2), and Acinetobacter sp. ADP-1 (Ac alkM). In addition, primers and probes detecting aromatic dioxygenase genes were derived from P. putida ATCC 17484 (ndoB), P. putida F1 (todC1), P. putida ATCC 33015 (xylE and cat23), and P. pseudoalcaligenes KF707 (bphA). The primers and probes were used to analyze total community DNA extracts by using PCR and hybridization analysis. All the catabolic genes, except the Ac alkM, were detected in contaminated and control soils from both geographic regions, with a higher frequency in the Antarctic soils. The alkane monooxygenase genes, Rh alkB1 and Rh alkB2, were the most frequently detected alk genes in both regions, while Pp alkB was not detected in Brazil soils. Genes encoding the aromatic dioxygenases toluene dioxygenase (todC1) and biphenyl dioxygenase (bphA) were the most frequently detected in Antarctica, and todC1 and catechol-2,3-dioxygenase (cat23) were the most frequent in Brazil soils. Hybridization analysis confirmed the PCR results, indicating that the probes used had a high degree of homology to the genes detected in the soil extracts and were effective in detecting biodegradative potential in the indigenous microbial population.     

A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania

Modern humans reached Southeast Asia and Oceania in one of the first dispersals out of Africa. The resulting temporal overlap of modern and archaic humans-and the apparent morphological continuity between them-has led to claims of gene flow between Homo sapiens and H. erectus. Much more recently, an agricultural technology from mainland Asia spread into the region, possibly in association with Austronesian languages. Using detailed genealogical study of Y chromosome variation, we show that the majority of current Austronesian speakers trace their paternal heritage to Pleistocene settlers in the region, as opposed to more-recent agricultural immigrants. A fraction of the paternal heritage, however, appears to be associated with more-recent immigrants from northern populations. We also show that the northern Neolithic component is very unevenly dispersed through the region, with a higher contribution in Southeast Asia and a nearly complete absence in Melanesia. Contrary to claims of gene flow (under regional continuity) between H. erectus and H. sapiens, we found no ancestral Y chromosome lineages in a set of 1,209 samples. The finding excludes the possibility that early hominids contributed significantly to the paternal heritage of the region.     

Questions of khoesan continuity: Dental affinities among the indigenous holocene peoples of South Africa

The present report follows up on the findings of previous research, including recent bioarchaeological study of well‐dated Khoesan skeletal remains, that posits long term biological continuity among the indigenous peoples of South Africa after the Pleistocene. The Arizona State University Dental Anthropology System was used to record key crown, root, and intraoral osseous nonmetric traits in six early‐through‐late Holocene samples from the Cape coasts. Based on these data, phenetic affinities and an identification of traits most important in driving intersample variation were determined using principal components analysis and the mean measure of divergence distance statistic. To expand biological affinity comparisons into more recent times, and thus preliminarily assess the dental impact of disproportionate non‐Khoesan gene flow into local peoples, dental data from historic Khoekhoe and San were also included. Results from the prehistoric comparisons are supportive of population continuity, though a sample from Matjes River Rockshelter exhibits slight phenetic distance from other early samples. This and some insignificant regional divergence among these coastal samples may be related to environmental and cultural factors that drove low‐level reproductive isolation. Finally, a close affinity of historic San to all samples, and a significant difference of Khoekhoe from most early samples is reflective of documented population history following immigration of Bantu‐speakers and, later, Europeans into South Africa. Am J Phys Anthropol 155:33–44, 2014. © 2014 Wiley Periodicals, Inc.     

Tropical forest recovery from logging: a 24 year silvicultural experiment from Central Africa

Large areas of African moist forests are being logged in the context of supposedly sustainable management plans. It remains however controversial whether harvesting a few trees per hectare can be maintained in the long term while preserving other forest services as well. We used a unique 24 year silvicultural experiment, encompassing 10 4 ha plots established in the Central African Republic, to assess the effect of disturbance linked to logging (two to nine trees ha⁻¹ greater than or equal to 80 cm DBH) and thinning (11–41 trees ha⁻¹ greater than or equal to 50 cm DBH) on the structure and dynamics of the forest. Before silvicultural treatments, above-ground biomass (AGB) and timber stock (i.e. the volume of commercial trees greater than or equal to 80 cm DBH) in the plots amounted 374.5 ± 58.2 Mg ha⁻¹ and 79.7 ± 45.9 m³ ha⁻¹, respectively. We found that (i) natural control forest was increasing in AGB (2.58 ± 1.73 Mg dry mass ha⁻¹ yr⁻¹) and decreasing in timber stock (−0.33 ± 1.57 m³ ha⁻¹ yr⁻¹); (ii) the AGB recovered very quickly after logging and thinning, at a rate proportional to the disturbance intensity (mean recovery after 24 years: 144%). Compared with controls, the gain almost doubled in the logged plots (4.82 ± 1.22 Mg ha⁻¹ yr⁻¹) and tripled in the logged + thinned plots (8.03 ± 1.41 Mg ha⁻¹ yr⁻¹); (iii) the timber stock recovered slowly (mean recovery after 24 years: 41%), at a rate of 0.75 ± 0.51 m³ ha⁻¹ yr⁻¹ in the logged plots, and 0.81 ± 0.74 m³ ha⁻¹ yr⁻¹ in the logged + thinned plots. Although thinning significantly increased the gain in biomass, it had no effect on the gain in timber stock. However, thinning did foster the growth and survival of small- and medium-sized timber trees and should have a positive effect over the next felling cycle.     

Phylogeography of Camassia quamash in western North America: postglacial colonization and transport by indigenous peoples

Recent human activities have spread numerous plant species across the globe, yet it is unclear to what degree historical human activities influenced plant dispersal. In western North America, Camassia quamash was one of the most important food plants for indigenous peoples, who transported its propagules either intentionally or accidentally. We investigated how human and natural dispersal might have contributed to the current pattern of spatial genetic structure in C. quamash by performing phylogeographical surveys at two geographical scales. We sequenced two noncoding regions of chloroplast deoxyribonucleic acid (DNA) in 226 individuals from 53 populations of C. quamash as well as 126 individuals from 21 populations of the non-food plant Zigadenus venenosus . Contrary to the expectation of anthropogenic transport, C. quamash populations did not exhibit weaker genetic structure than Z. venenosus populations. We also failed to find convincing evidence for signatures of transport. Instead, our data showed strong effects of past glaciation and geographical barriers of the mountains in the Cascade Range, Olympic Peninsula and Vancouver Island. West of the Cascades, the species appears to have largely migrated northward from a southern refugium after deglaciation, whereas few populations having a highly divergent haplotype might have survived in southwestern Washington. Our data suggest that despite substantial ethnobotanical evidence for anthropogenic transport, the current pattern of genetic structure of C. quamash does not show any detectable signatures of transport by indigenous peoples and is better understood as the result of natural dispersal processes.     

Karyology of the Atlantic forest rodent Juliomys (Cricetidae): A new karyotype from southern Brazil

Juliomys is a small rodent from the family Cricetidae which inhabits the Atlantic forest and forests from Argentina to eastern Brazil. The three species recognized so far have different karyotypes. In this paper, we describe a new karyotype with 2n = 32, FN = 48 found in Juliomys specimens from a high-altitude area in the Atlantic forest of southern Brazil. The karyotype was analyzed after G- and C-banding and silver staining of the nucleolus organizer regions (Ag-NOR) and its G-banding patterns were compared with those of the newly described species Juliomys ossitenuis (2n = 20, FN = 36). The 2n = 32 karyomorph presented peculiar features and was very different from those of the other species of the genus: J. pictipes (2n = 36, FN = 34), J. rimofrons (2n = 20, FN = 34) and J. ossitenuis (2n = 20, FN = 36). Differences were mostly due to centric and tandem fusions, pericentric inversion and loss of heterochromatin. The karyotype represents a powerful tool to differentiate Juliomys species and our data suggest that the karyotype described herein belongs to a new species.     

森林采伐对尖峰岭海南特有种子植物多样性的影响

特有种子植物是热带森林植物区系的一个重要组成部分,且很容易受到人为干扰的影响,但是森林采伐对特有种子植物的影响少有报道。本文基于164个25m×25m植被公里网格样地数据,分析了海南岛尖峰岭地区海南特有种子植物(以下简称特有种子植物)的组成结构、样地内特有种子植物物种数与总物种数之间的关系;并从种-面积曲线、累积种-个体关系和物种多度分布3个方面比较了原始林、径级择伐林和皆伐林样地中特有种子植物的物种多样性变化规律。结果显示:尖峰岭地区特有种子植物种类丰富,共有158种,占全岛(397种)的40%;其中木本特有种子植物达98种(藤本除外),在164个样地内共记录到胸径≥1.0cm的52种,占整个尖峰岭地区的53%,以樟科、壳斗科、茜草科种类为主。样地内特有种子植物的物种数与总物种数成正相关关系。采伐后特别是径级择伐后特有种子植物物种数略微增加,但增加的种类大多仅在1-2个样地中出现;而且种群也比较小,表现为较稀有且不稳定的种群结构特征,在后续的更新中消失的可能性较大。但是,采伐后一些特有种子植物仍具有中等大小的种群,例如毛荔枝(Nephelium topengii)、海南紫荆木(Madhucaha inanensis)和尖峰岭锥(Castanopsis jianfenglingen-sis)等。     

Changes in the forest floor of Canadian southern boreal forest after disturbance

Abstract. The concentrations and contents of organic matter and nutrients in organic deposits on the forest floor were estimated along a 231-yr chronosequence following fire at the southern limit of the boreal forest in eastern Canada. The sampling design was stratified to take into account the variability related to the presence of the principal tree species as well as to the presence of large gaps created by a recent spruce budworm (Choristoneura fumiferana) outbreak. The forest floor showed a steady accumulation of organic matter and total nutrients with time-since-fire and a 50 % decrease in the concentrations of available P and K, but not N (as determined by aerobic incubation). The increase in forest-floor weight was accompanied by an increased storage of available N, Ca and Mg. The availability of N and Ca was more strongly affected by tree species and gaps than by time-since-fire. A high N-availability was observed under Betula papyrifera and in gaps, while high a Ca-availability was found near Populus tremuloides and Thuja occidentalis. In old sites, the forest floor of gaps, created by a recent spruce budworm outbreak, had a necromass similar to that of a young forest, but the low concentrations of available P and K of an old forest.     

A footprint of tree‐genetics on the biota of the forest floor

Understanding how far the effects of genes extend beyond the phenotype of an individual or population, is fundamental to the developing field of community genetics. We therefore assessed two geographically and genetically distinct populations of the Australian forest tree, Eucalyptusglobulus, and the existence of genetic effects on a leaf litter invertebrate community and soil characteristics within a 15 year old common garden. Twenty trees per population were randomly selected for felling and placement of the apical branch next to the stump. This produced a leaf litter habitat of known genotype. Pitfall trap sampling for invertebrates, and linseed bioassay analyses of soil, were conducted within this habitat. Two key findings emerged. Firstly, assessment of 27 invertebrate orders (57 924 individuals) revealed significant population‐level variation in leaf litter biodiversity (i.e. in community richness, abundance, composition and beta diversity). Secondly, considerable population‐level differences in soil characteristics were evident based on linseed germination and growth responses. While recent findings in E. globulus have demonstrated consequences of genetic variation within forest trees for organisms that interact directly (i.e. proximally) with the living tree, these findings highlight the distal impacts that intraspecific genetic variation may have on communities and ecosystems. Such community genetic considerations have important implications for in situ community conservation, biodiversity management within restoration and plantation forestry, and our understanding of community‐level evolutionary interactions involving foundation species.     

Organic matter and nutrient dynamics of the forest and forest floor in the Hubbard Brook forest

Summary The forest floor is a major reservoir of organic matter and nutrients for the ecosystem and as such it influences or regulates most of the functional processes occurring throughout the ecosystem. This study reports on the nutrient and organic matter content of the forest floor of the Hubbard Brook Experimental Forest during different seasons and attempts to correlate results from studies of vegetation, litter, decomposition, stemflow, throughfall, and soil. An organic matter budget is presented for an undisturbed watershed.Average weight of the forest floor on an undisturbed watershed ranged from 25,500 to 85,500 kg/ha. The weighted watershed average was 46,800 kg/ha. Although the F and H horizons did not vary significantly with time, the L horizon increased significantly during the period June to August largely as a result of a severe hail storm. The order of abundance of elements in the forest floor was N;CaFe>S>P>Mn>K>Mg>Na>Zn>Cu. The concentrations of Ca, K, and Mn decreased with depth in the forest floor while N, P, S, Na, Fe, Zn, and Cu concentrations increased. N:P ratios were similar in decomposing leaf tissue, the forest floor, litterfall, and net stemflow plus throughfall suggesting a similar pattern of cycling. S was proportional to N and P in decomposing leaf tissue, the forest floor, and litterfall. Net stemflow and throughfall were affected by a relatively large input of SO₄=-S from the atmosphere. Residence times for elements in the forest floor were affected by inputs other than litterfall (precipitation, stemflow, and throughfall). Calculation of residence times using all inputs caused smaller values than if litterfall alone was used. While all residence times were reduced, the major differences occurred for K, S, and Na. N and P showed relatively long residence times as a result of retranslocation and immobilization by decomposers. The slow turnover rate because of the strong demand and retention by all biota must account for the efficiency of the intrasystem cycling process for N and P. K showed the shortest residence time. A rapid and efficient uptake of K by vegetation seems to account for the efficient cycling of this element. The patterns of nutrient cycling are several depending on the chemical properties of the forest floor, and nutritional requirements of the biota.This is contribution No. 67 of the Hubbard Brook Ecosystem Study. Financial support was provided by the National Science Foundation.     

Watershed liming effects on the forest floor N cycle

The forest floor was expected to play a major role in determining the total ecosystem response to watershed liming because of its high concentration of nutrients and its high level of activity. Net N mineralization and net nitrification were estimated in a field survey using the buried-bag approach. In a laboratory incubation experiment, forest floor humus was mixed with 6 doses of lime to determine the sensitivity of N mineralization and nitrification to lime dose. Forest floor microcosms with and without live tree roots were used to calculate a N budget for the system.The pH of the forest floor increased from 3.6 to 4.9 in the Oe and to 4.0 in the Oa two years after liming. The extractable ammonium pool in both the field survey and microcosm study was substantially smaller after liming and was probably a result of the 36% to 55% lower net N mineralization rate in limed plots than in reference plots. The laboratory incubation results agreed with the field survey results and further demonstrated that at higher lime doses (pH 5 to 6), N mineralization increased above controls. Net nitrification in limed humus in both the buried bags and laboratory incubation was as much as three times higher than controls, which could explain why nitrate leaching in limed microcosms was greater than in control microcosms. However, nitrate leaching from microcosms with live. roots was not affected by liming, suggesting that roots in the forest floor may prevent excess nitrate leaching. Reductions in N mineralization had no effect on N leaching or N uptake, but reduced the extractable ammonium pool.