Geophagic termite mounds as one of the resources for African elephants in Ugalla Game Reserve,Western Tanzania

Knowledge of the distribution and nutrient values of key resources supporting the survival of wildlife species is integral for an effective conservation planning and management of the species. In the Miombo ecosystem of the Ugalla Game Reserve, African elephants (Loxodonta africana Blumenbach 1797), eat soil, that is geophagy, from certain termite mounds. We mapped that all the geophagic termite mounds are exclusively situated in the flood plain. To understand why soils from some termite mounds are eaten, we collected and analysed soil samples from 10 geophagic termite mounds, seven nongeophagic termite mounds and 13 samples from the surrounding flood plain. Percentage of clay content did not differ significantly among the soil samples. Soils from geophagic termite mounds were richer in mineral elements compared with other soil samples. The results demonstrate that the driver for geophagic behaviour is related to rich mineral element contents found in geophagic termite mounds made of the mineral‐enriching termites (Macrotermes). Thus, geophagic termite mounds play a role in elephant's dietary needs and possibly influence their movement patterns in Ugalla, as the elephants cannot obtain enough minerals from their feeds. Geophagic termite mounds should be protected from potential destructive land uses, such as airstrip construction.     

Assessing the function of geophagy in a Malagasy rain forest lemur

Geophagy has been observed in nearly every long‐term study of folivorous primates. Yet despite frequent observations of this behavior, conclusive explanations for soil consumption remain ambiguous. This study tests the most frequently proposed hypotheses for geophagy using data collected on the geophagic behavior of the Milne‐Edwards’ sifaka (Propithecus edwardsi) living in two forests with varying levels of disturbance within Ranomafana National Park, Madagascar. Field data were collected from December 2002 to November 2003, during which time soil samples were collected for mineral analyses from 102 sites selected for geophagy and 42 control sites at which no geophagy was recorded. Results indicate that control soils differ significantly between the two study sites and that this difference is primarily attributable to varying levels of habitat disturbance. The frequency of soil consumption also does not vary significantly by sex or between logged and unlogged habitats. Soil consumption significantly correlated with fruit/seed consumption overall, but to a lesser degree in logged compared with unlogged sites. Clay minerals found in soils likely prevent absorption of dietary toxins in the gut and/or may mediate gut pH. This provides strong evidence for the protection hypothesis for geophagy, which may be especially important in areas where logging, or other forms of habitat disturbance, has been experienced. Abstract in French is available with online material.     

Soil seed bank characteristics in Cameroonian rainforests and implications for post-logging forest recovery

The soil seed bank is considered as an important component for resilience of climacic vegetation. Whereas several related studies have been conducted in Asian, American and some African tropical forests, no investigation has ever been conducted in Central African rainforests, especially in logged forests where the soil seed bank could contribute to regeneration of timber of trees species. We studied the soil seed bank characteristics in relation to the standing vegetation in three Cameroonian forest zones with different disturbance regimes. There was no significant difference between sites in terms of density of the seed bank; the average mean density was 87.6 seeds m⁻². But dissimilarities of the floristic compositions between sites were quite high. Overall, seeds came from 43 species including three commercial tree species. Whereas the seedlings emerging from soil samples mostly came from weedy and short-lived pioneer species, climax species predominated in the extant vegetation, leading to a very weak similarity between soil seed flora and the surrounding vegetation: Sorensen's index ranged from 3.5 to 7.6%. Canopy openness could significantly affect the species richness of soil seed stocks but not the seed density. These results show that the soil seed bank contribution to the resilience of mature tropical forests is low. In particular, very few timber tree species could benefit from soil seed stocks for their regeneration. Therefore, the development of enrichment techniques including use of the soil seed bank as a source of tree regeneration in such a context would be irrelevant.     

Riparian Forest Restoration Along Large Rivers: Initial Results from the Sacramento River Project

Restoration of riparian vegetation along large rivers is complicated by the patchiness of the habitat and by conflicts with the societal need to control flooding. The Sacramento River Project, led by The Nature Conservancy in northern California, is testing whether it is possible to restore native forest along a large river without removing flood control. We conducted a post-hoc analysis of monitoring data collected by the project on 1–4-year old plantings of 10 native trees and shrubs at five sites. Two questions of general interest were: Can one identify types of species or sites that are especially suitable for restoration in such riparian habitats? To what degree must sites be treated as mosaics of patches, with different types of patches that are suited to different species? Plant performance as measured by height was better in species of Salicaceae or in species planted as cuttings than in species of other families or in species planted as seedings or seeds. Three within-site factors, land form, soil depth to a buried layer of sand or gravel, and soil texture, affected the growth of several species, indicating that sites do need to be treated as patchy. However, there was little evidence that different species performed better on different types of patches. Instead, areas with deep or fine soils seemed to be favorable for a number of species. Results suggest that it is feasible to re-establish native trees and shrubs along large, regulated rivers, at least at certain sites for an initial period of several years with the aid of weed control and irrigation. Shallowly buried layers or lenses of gravel or sand are a hidden, fine-scale factor that can reduce plant growth on river terraces.     

Microhabitat determines how grazing affects bryophytes in wood-pastures

Wood-pastures are biodiverse biotopes where livestock graze among trees. The diversity of several species groups is related to the structural diversity created by herbivores and by trees, decaying wood and rocks. One of the greatest threats to wood-pastures is abandonment that results in decreased heterogeneity of soil microhabitats as well as encroachment by young trees. We studied the diversity of bryophytes on different microhabitat types (soil, rocks, trees and decaying wood) in grazed and abandoned boreal wood-pastures (48 sites). Most species grew on soil, rocks or both. For both soil and rocks currently grazed sites had higher bryophyte species richness and several individual species also preferred grazed sites over abandoned sites. The grazers increase biodiversity by creating patches of bare soil and exposed rock surfaces. Currently grazed and abandoned sites did not differ significantly in bryophyte species richness on decaying wood or trees, and the overall bryophyte richness on these substrates was quite low due to the scarcity of dead wood and large living deciduous trees with suitable bark conditions. Rare species were observed on all microhabitats, most abundantly on soil and decaying wood. Especially our result on higher richness on rock surfaces shows the complexity of grazing effects on biodiversity. Grazers may affect the biodiversity of a species group that is not consumed by them, on a surface which is not attractive to them. These unobvious interactions should be recalled when planning wood-pasture management and conservation.     

The use of a functional approach as surrogate of Collembola species richness in European perennial crops and forests

Collembolans are known indicators of soil disturbance, used in several soil biodiversity monitoring programmes. As for other groups of soil microarthropods, taxonomic determination of Collembola species requires a huge effort and expert knowledge. In this study, we evaluated whether identification of Collembola species to the morphotype level, using an eco-morphological index which classifies individuals based on their adaptation to the soil, can be used as a surrogate of species richness in extensive monitoring schemes. The same evaluation was performed for higher taxa surrogates, using taxonomic categories at the genus and family levels. Additionally, sampling effort for perennial crops and forest systems was determined. Species data were collected from 35 sites sampled within different projects with the same number of samples (16 per site). Results showed that, on average, 8–12 samples are enough to have a good estimate of species richness for this type of systems, averaging 80–90%, but varying considerably with site habitat heterogeneity and local Collembola species pool. GLM models (using species richness as response variable) fitted for family, genus or morphotype levels (explanatory variables) were all significant (p < 0.05) but only the latter two had a pseudo R² higher than 0.75. This indicates that when a rapid, cost-effective assessment of Collembola richness in different sites is required, this eco-morphological trait approach, as well as the determination to the genus level, could be used.     

Forest biomass,soil and biodiversity relationships originate from biogeographic affinity and direct ecological effects

Ecosystem biomass, soil conditions and the diversity of different taxa are often interrelated. These relationships could originate from biogeographic affinity (varying species pools) or from direct ecological effects within local communities. Disentangling regional and local causes is challenging as the former might mask the latter in natural ecosystems with varying habitat conditions. However, when the species pool contribution is considered in statistics, local ecological effects might be detected. In this study we disentangle the indirect effects of the species pool and direct ecological effects on the complex relationships among wood volume, soil conditions and diversities of different plant and fungal groups in 100 old‐growth forest sites (10 × 10 m) at the border of boreal and nemoral zones in northern Europe. We recorded all species for different vegetation groups: woody and herbaceous vascular plants, terricolous and epiphytic bryophytes and lichens. Fungal communities were detected by DNA‐based analyses from soil samples. Above‐ground wood volume was used as a proxy of biomass. We measured soil pH and nutrient content and obtained modelled climate parameters for each site. Species pool effect was considered by dividing sites into boreal and nemoral groups based on community composition. In order to disentangle direct and indirect effects, we applied variation partitioning, and raw and partial correlations. We found many significant positive relationships among studied variables. Many of these relationships were associated to boreal and nemoral species pools, thus indicating that biogeographic affinity of interacting plants and fungi largely defines forest diversity and functioning. At the same time, several relationships were significant also after considering biogeography: woody plant and ectomycorrhizal fungi diversities with wood volume, many plant and fungal groups with each other, or with soil conditions. These direct ecological interactions could be considered in forestry practices to achieve both economic gain and maintenance of biodiversity.     

Geophagy by African ungulates: the case of the critically endangered giant sable antelope of Angola (Hippotragus niger variani)

The giant sable antelope (Hippotragus niger variani) is a critically endangered subspecies with a range restricted to a small area in the Angolan plateau. It is known to display geophagic behaviour, eating the soil of some Macrotermes termitaria. The aim of this study was to understand the importance of this behaviour for the giant sable and other ungulates sharing its range. We identified termite mounds used for geophagy based on local information confirmed by self‐triggering cameras. We collected and analysed soil samples of seven termitaria consumed by ungulates, the adjacent topsoil 50 m away from each, and seven control nonconsumed termitaria. Consumed termite mounds were richer in minerals than control mounds, and both were richer than the surrounding topsoil. Sodium levels showed the greatest contrasts and were about 20 times more abundant in consumed termitaria than in controls. The amount of sodium in background soil was extremely low (9.3 ppm), suggesting that this mineral is a limiting nutrient in the range of the giant sable. These results indicate that the observed geophagic habits may be driven by a need to compensate for a sodium deficiency. This situation should be considered in the planning of the species' conservation.     

The occurrence of keratinophilic fungi in queensland

Summary Keratinophilic fungi have been isolated and identified in soil samples from 233 sites in Queensland and 12 from the Northern Territory. Total numbers of the fungi isolated are given, together with their occurrence in various broad types of locality.It is noted that populated localities produced a higher incidence of keratinophilic fungi than remote areas. Exceptions to this were found in beach sand, 17 samples of which produced only two growths ofChrysosporium species and no potentially pathogenic fungi.Culture technique, and the method of examination of colonies are discussed, and the morphological features of several of the more commonly occurring species are described.Isolates ofChrysosporium tropicum were made from two samples, one from Alice Springs and one from Brisbane. This is the first time this fungus has been reported in Australia.     

土壤纤毛虫群落对退牧还草生态恢复的响应——以玛曲县为例

为研究退牧还草对土壤纤毛虫群落特征的影响、退牧还草后土壤环境变化以及如何利用原生动物纤毛虫群落特征来评价退还效果的可行性,于2015年5月至2016年3月在甘肃省甘南藏族自治州玛曲县选取3个不同恢复年限的草地样点和1个未经过退牧还草对照样点,采用"非淹没培养皿法"、活体观察法和培养直接计数法对土壤纤毛虫的物种数和密度进行测定,同时测定了土壤温度、pH值、含水量、土壤孔隙度、速效钾、速效氮、速效磷、全氮、全钾、全磷和有机质含量,并分析了在生态逐渐恢复条件下,土壤纤毛虫群落特征与土壤环境因子间的相关性。研究共鉴定到纤毛虫95种,隶属9纲15目21科28属。研究发现,退牧还草样地与未退牧还草样地的土壤纤毛虫的物种分布存在明显差异:退牧还草后的3个样点间的物种相似性减小,群落组成复杂化,纤毛虫丰度、丰富度指数、均匀度指数和物种多样性指数增高。相关性分析结果表明,退牧还草后,对纤毛虫群落结构稳定性影响最主要的是土壤有机质、含水量和土壤全氮、全磷和全钾的含量,不同恢复年限样点的土壤纤毛虫群落组成差异较大。土壤纤毛虫群落对退牧还草生态恢复过程中土壤环境条件的变化有较好的响应。     

Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon Cascade Mountains

Although nitrification has been well studied in coniferous forests of Western North America, communities of NH(3)-oxidizing bacteria in these forests have not been characterized. Studies were conducted along meadow-to-forest transects at two sites (Lookout and Carpenter) in the H. J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon. Soil samples taken at 10- or 20-m intervals along the transects showed that several soil properties, including net nitrogen mineralization and nitrification potential rates changed significantly between vegetation zones. Nonetheless, terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR-amplified NH(3) monooxygenase subunit A gene (amoA) showed the same DNA fragments (TaqI [283 bp], CfoI [66 bp], and AluI [392 bp]) to dominate >/=45 of 47 soil samples recovered from both sites. Two fragments (491-bp AluI [AluI491] and CfoI135) were found more frequently in meadow and transition zone soil samples than in forest samples at both sites. At the Lookout site the combination AluI491-CfoI135 was found primarily in meadow samples expressing the highest N mineralization rates. Four unique amoA sequences were identified among 15 isolates recovered into pure culture from various transect locations. Six isolates possessed the most common T-RFLP amoA fingerprint of the soil samples (TaqI283-AluI392-CfoI66), and their amoA sequences shared 99.8% similarity with a cultured species, Nitrosospira sp. strain Ka4 (cluster 4). The other three amoA sequences were most similar to sequences of Nitrosospira sp. strain Nsp1 and Nitrosospira briensis (cluster 3). 16S ribosomal DNA sequence analysis confirmed the affiliation of these isolates with Nitrosospira clusters 3 and 4. Two amoA clone sequences matched T-RFLP fingerprints found in soil, but they were not found among the isolates.     

黄山短尾猴食土行为

从行为生态学角度,依据黄山短尾猴食土行为在年龄、性别、社会等级序位、食土量、食土频率、食土持续时间中的分布和变化规律,结合土壤基本理化性质测定和分析,探讨了黄山短尾猴食土行为。黄山短尾猴对土壤的摄取是寻找和有目的的选择,有些场所是其"喜好"或"常去之处",食土场所通常是以多个体多次取食挖掘而形成的洞穴形式存在。取食土壤颜色黄色或黄棕色,酸性土壤,富含铁、钙、镁等矿物元素,粘土比例较高。社群各年龄段及性别个体均参与食土行为。平均食土行为持续时间在年龄和性别之间无显著差异;平均食土频率和食土量在成年雌性或雄性个体的社会等级序位之间无显著性差异;而成年雌性的平均食土频率和食土量,显著高于其它年龄或性别组,与雌性正值怀孕末期及产仔哺乳期,需要补充大量铁等矿物元素,以维持生理所需和体力消耗有关。典型的植食性动物黄山短尾猴有规律地取食粘土的行为,支持了食土行为具有"食物解毒作用"假说。人工投喂和食土行为的相关性表现为提高了食土频率,可能与粘土能够缓解高热量、低纤维人工食物造成的胃肠不适有关。     

Quantification of the slug parasitic nematode Phasmarhabditis hermaphrodita from soil samples using real time qPCR

Phasmarhabditis hermaphrodita is a nematode parasite that infects and kills several species of slugs. The nematode is produced commercially as a biological control agent for slug pests of agriculture and horticulture. Given the difficulties of distinguishing this species from other nematode species in soil samples, very little is known about its natural ecology or its behaviour and persistence following application for biological control. Here we describe a method to quantify P. hermaphrodita in soil samples based on real time PCR. We designed primers and a dual labelled fluorescent probe that can be used to quantify numbers of P. hermaphrodita and which is capable of distinguishing this species from the morphologically identical Phasmarhabditis neopapillosa. We compared different methods whereby the entire nematode community is extracted prior to DNA extraction, and three methods to extract DNA directly from soil samples. Both nematode extraction and DNA extraction from large (10 g) samples of soil gave reliable estimates of nematode numbers, but methods which extracted DNA from small (1 g or less) soil samples substantially underestimated numbers. However, direct extraction of DNA from soils may overestimate numbers of live nematodes as DNA from dead nematodes was found to persist in soil for at least 6 days. The technique could be modified for detection and quantification of all soil borne parasitic nematodes.     

Disturbance Effects on the Seed Bank of Mexican Cloud Forest Fragments1

The density and floristic composition of the soil seed bank was assessed in six cloud forest fragments with different levels of human disturbance in central Veracruz, Mexico. A total of 8416 seeds germinated in 60 soil samples, at 5‐cm depth, corresponding to 107 species, 85 genera, and 48 families. Significant differences were found among study sites in seed densities with values ranging from 873 to 3632/m². Tree species contributed 20 percent of the total soil seed bank in four sites and herbs accounted for the majority of the species in each site. Among tree species, Trema micrantha displayed the highest seed density, accounting for 84 percent of the germinated seeds. In general, the tree species composition of the soil seed bank did not closely reflect the composition of the tree community. Results suggest that disturbance produced by human activities (trail use, selective cutting of trees, livestock) may influence the size and composition of the soil seed bank in forest fragments. Sites where human activity has been reduced showed the highest proportion of dormant seeds.     

Beta‐Diversity of Termite Assemblages Among Primary French Guiana Rain Forests

Termites are an important component of tropical rain forests, and have been included in many studies focusing on the influence of human disturbance. Their distribution among primary rain forest has, however, rarely been investigated. Here we studied the termite fauna in seven mostly undisturbed forest sites, representing several rain forest types. Overall, approximately 70 percent of species were soil‐feeders and 25 percent were wood‐feeders, the remaining 5 percent being classified here as litter‐feeders. Termite species richness did not differ significantly among sites, but sites differed in termite abundance. The palm swamp and the low forest situated on the foothills of an inselberg, hosted different termite communities to the other sites. These two sites presented a singular physiognomy suggesting that forest type is an important factor influencing species composition. We found no correlation between termite species composition and distance between sites, highlighting that at the scale of our study (about 100 km), forest sites share a similar species pool.     

Indigenous hydrocarbon-utilizing bacterioflora in oil-polluted habitats in Kuwait, two decades after the greatest man-made oil spill

Kuwaiti habitats with two-decade history of oil pollution were surveyed for their inhabitant oil-utilizing bacterioflora. Seawater samples from six sites along the Kuwaiti coasts of the Arabian Gulf and desert soil samples collected from seven sites all over the country harbored oil-utilizing bacteria whose numbers made up 0.0001-0.01% of the total, direct, microscopic counts. The indigenous bacterioflora in various sites were affiliated to many species. This was true when counting was made on nitrogen-containing and nitrogen-free media. Seawater samples harbored species belonging predominantly to the Gammaproteobacteria and desert soil samples contained predominantly Actinobacteria. Bacterial species that grew on the nitrogen-free medium and that represented a considerable proportion of the total in all individual bacterial consortia were diazotrophic. They gave positive acetylene-reduction test and possessed the nifH genes in their genomes. Individual representative species could utilize a wide range of aliphatic and aromatic hydrocarbons, as sole sources of carbon and energy. Quantitative determination showed that the individual species consumed crude oil, n-octadecane and phenanthrene, in batch cultures. It was concluded that the indigenous microflora could be involved in bioremediation programs without bioaugmentation or nitrogen fertilization. Irrigation would be the most important practice in bioremediation of the polluted soil desert areas.     

Invasion of exotic plants in nutrient‐enriched urban bushland

Abstract Invasion of exotic plants into vegetation communities on low‐nutrient soils in Sydney is often attributed to increased phosphorus in the soil. However, the composition of native vegetation in nearby national parks has been found to be more closely correlated to combinations of soil nutrients and other environmental variables than phosphorus alone. This study examined whether phosphorus or a range of variables better matched patterns of native and exotic plants in urban bushland. Sites in urban bushland and national parks were sampled, vegetation frequency recorded and soil samples collected. Soil samples were analysed for a range of chemical and physical attributes. A significantly greater number of exotic species were found at the urban sites, and significantly fewer native species than in the national parks. All measured soil nutrients were found to be of a significantly increased concentration in urban soil. Using regression analysis, an index of all measured soil nutrients was found to explain more of the variation in the percentage of exotic species at a site than phosphorus alone. Multivariate analysis showed a gradient of sites from minimal exotic invasion to heavy invasion. However, this gradient also corresponded to changes in native species. The gradient was found to match that of increasing soil nutrient levels. A combination of soil nutrients was found to correlate better with the multivariate species composition than was phosphorus alone. The results suggest that it is the increase of many soil nutrients, not phosphorus alone, that is contributing to the invasion of urban bushland by exotic plants and the alteration of the suite of native species.     

PCR-DGGE Comparison of Bacterial Community Structure in Fresh and Archived Soils Sampled along a Chihuahuan Desert Elevational Gradient

The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation of long-term patterns in bacterial species richness and community structure that was not available with previous technology. However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing microbial community dynamics for particular ecosystems or landscapes.     

Preliminary assessment of arbuscular mycorrhizal fungal diversity and community structure in an urban ecosystem

Arbuscular mycorrhizal fungal (AMF) species richness, composition, spore density and diversity indices were evaluated in the Phoenix metropolitan area, Arizona, USA at 20 sampling sites selected to represent the four predominant land-use types found in the greater urban area: urban-residential, urban non-residential, agriculture and desert. AMF spores were extracted and identified from soil samples and from trap cultures established using soil collected at each site. Data were analyzed according to land use, land-use history, soil chemistry and vegetation characteristics at each site. Current agricultural sites were associated with decreased spore densities and historically agricultural sites with decreased species richness. Overall species composition was similar to that previously reported for the Sonoran desert, but composition at each sampling site was influenced by the vegetation from which samples were collected. Sites with the highest degrees of similarity in AMF species composition were also similar to each other in native plants or land use. Conversely, sites with the lowest similarity in AMF composition were those from which the majority of samples were collected from non-mycorrhizal plants, predominately ectomycorrhizal plants or bare soil. Spores of Glomus microggregatum were most abundant in urban sites, while those of G. eburneum were most abundant in desert and agricultural sites. Further studies are needed to determine the functional implications of shifts in AMF communities in urban ecosystems, including effects on plant primary productivity.     

连作苹果园土壤真菌的T-RFLP分析

为探讨连作苹果园不同土壤空间真菌群落结构,应用T-RFLP(Terminal Restriction Fragment Length Polymorphism)技术,比较了3个连作园不同取样位置(行间、原穴、株间)和不同土层(0—30 cm、30—60 cm)的土壤真菌多样性,并结合不同样品TRFLP图谱的差异,采用多样性指数分析、聚类分析和主成分分析(PCA),分析了3个连作园土壤真菌群落结构特征。结果表明,磁窑、道朗和金城连作园的土壤真菌多样性存在差异,各采样地区的Shannon多样性指数在0.43—2.47之间,Pielou均匀度指数在0.17—0.85之间,Simpson优势度指数在0.12—0.81之间,Margalef丰富度指数最高的是金城树穴0—30 cm土层(R=4.55),最低的是磁窑行间30—60 cm土层(R=0.77)。在调查的不同取样位置、不同土层中,原树穴具有最高的多样性指数、均匀度指数、丰富度指数和最低的优势度指数;0—30 cm土层的土壤真菌多样性指数、均匀度指数、丰富度指数均高于30—60cm土层,而优势度指数的趋势正好相反;PCA和聚类分析结果显示磁窑、道朗和金城连作园的土壤真菌群落结构均有明显差异,3个连作园的土壤真菌各自构成一个独立的群落结构,这些群落能够适应各自的土壤环境并成为环境的优势群落。