Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes

Since the endosymbiotic origin of chloroplasts from cyanobacteria 2 billion years ago, the evolution of plastids has been characterized by massive loss of genes. Most plants and algae depend on photosynthesis for energy and have retained ～110 genes in their chloroplast genome that encode components of the gene expression machinery and subunits of the photosystems. However, nonphotosynthetic parasitic plants have retained a reduced plastid genome, showing that plastids have other essential functions besides photosynthesis. We sequenced the complete plastid genome of the underground orchid, Rhizanthella gardneri. This remarkable parasitic subterranean orchid possesses the smallest organelle genome yet described in land plants. With only 20 proteins, 4 rRNAs, and 9 tRNAs encoded in 59,190 bp, it is the least gene-rich plastid genome known to date apart from the fragmented plastid genome of some dinoflagellates. Despite numerous differences, striking similarities with plastid genomes from unrelated parasitic plants identify a minimal set of protein-encoding and tRNA genes required to reside in plant plastids. This prime example of convergent evolution implies shared selective constraints on gene loss or transfer.     

Subterranean axes in tribe Diurideae (Orchidaceae): Morphology,anatomy, and SYSTEMATIC SIGNIFICANCE

The morphological and anatomical nature of perennating storage organs of the predominantly Australasian orchid tribe Diurideae (Orchidoideae: Orchidaceae) as well as anatomical concepts in tribes Orchideae and Diseae of Orchidoideae have been problematic for 150 yr, reflected in conflicting or vague terminology and questions about polystely and even monophyly of Orchidoideae. From a representative survey of underground organs of 145 species in 37 ingroup genera (Diurideae) and two outgroup genera (Spiranthes and Disa), the so-called “root-stem tuberoids” are here interpreted as root tubers (except for the stem tubers of Rhizanthella) borne on either droppers or stolonoid roots. All root tubers examined are bounded by a 1–4 layered velamen and exodermis, whereas droppers and stolonoid roots may have velamen-exodermis or a simple epidermis depending on the taxon and often bear multiseriate or uniseriate trichomes associated with mycorrhiza (as do roots of some taxa). The “polystely” reported in tubers of many Orchideae also occurs in tubers of many Diurideae but represents only dissection of the siphonostele into 2–13 traces. Cladistic analyses of data show extraordinarily high levels of homoplasy in characters related to root, dropper/stolonoid root, and tuber, so that these characters alone are of limited usefulness.     

Fluorine content in natural water in the southern Ob-Irtysh interfluve

Fluorine content in 327 sources of surface, soil-ground and underground water in the southern Ob-Irtysh interfluve has been studied. Fluctuations of fluorine concentration in water are rather considerable; their possible geochemical origins are considered. A large region with high (exceeding MPC) fluorine concentration in the sources of underground water involved in water supply to inhabited areas was discovered in the western Baraba plain. The fluorine/calcium ratios in those water samples evidence a high danger of fluorosis in the population.     

西部干旱区煤炭开采环境影响研究

大规模煤炭资源开采与干旱脆弱生态环境的空间耦合将会诱发日益严峻的社会、环境问题。分析了我国西部干旱区煤炭地下开采对植被、土壤水、地下水、土壤等关键环境要素影响的研究进展与不足;指出现有研究主要以单一环境要素、局部尺度为主,缺乏多尺度综合的环境要素协同损伤规律与井上下联动响应机理等基础研究。因此,现有成果还无法满足指导煤炭开采技术改进与控制环境损伤的需要。建议从井下到井上,从工作面、矿井、矿区、流域多尺度综合实现地空一体化同步监测,加强对西部干旱矿区各关键环境要素的协同损伤规律研究;加强对井上下环境要素对开采地质条件响应机理研究;建立不同开采条件、不同评价尺度下,矿区开采环境损伤的评价与预测模型。     

核桃-大豆间作系统细根分布及地下竞争

以晋西黄土区核桃-大豆间作系统为研究对象,采用分层挖掘法对核桃-大豆间作系统细根分布特征及地下竞争状况进行研究,旨在为该地区果农间作系统的高效可持续经营提供科学依据。结果表明:核桃细根在垂直方向上主要分布在0～40cm土层内,水平方向上55.7%的细根集中分布在距树行0.5～1.5m区域中;间作物大豆的根系在垂直方向上集中分布在0～20cm土层内,水平方向上根干重随距树行距离的增加呈增加趋势;在水平方向上距树行1.0～2.5m的区域是核桃和大豆地下种间竞争主要发生区,其中以1.5～2.0m区域的竞争最为剧烈。     

High‐resolution secondary ion mass spectrometry analysis of carbon dynamics in mycorrhizas formed by an obligately myco‐heterotrophic orchid

Mycorrhiza formation represents a significant carbon (C) acquisition alternative for orchid species, particularly those that remain achlorophyllous through all life stages. As it is known that orchid mycorrhizas facilitate nutrient transfer (most notably of C), it has not been resolved if C transfer occurs only after lysis of mycorrhizal structures (fungal pelotons) or also across the mycorrhizal interface of pre‐lysed pelotons. We used high‐resolution secondary ion mass spectrometry (nanoSIMS) and labelling with enriched ¹³CO₂ to trace C transfers, at subcellular scale, across mycorrhizal interfaces formed by Rhizanthella gardneri, an achlorphyllous orchid. Carbon was successfully traced in to the fungal portion of orchid mycorrhizas. However, we did not detect C movement across intact mycorrhizal interfaces up to 216 h post ¹³CO₂ labelling. Our findings provide support for the hypothesis that C transfer from the mycorrhizal fungus to orchid, at least for R. gardneri, likely occurs after lysis of the fungal peloton.     

Groundwater contamination with cadmium concentrations in some West U.P. Regions,India

Water is considered a vital resource because it is necessary for all aspects of human and ecosystem survival. However, due to natural processes and anthropogenic activities, various pollutants have been added to the ground water system. Among these, heavy metals are some of the most serious pollutants. Cd, a toxic heavy metal used in Ni-Cd batteries, the colouration of plastic and various discarded electronic products released into the water system causes serious health issues. The chronic exposure to Cd produces a wide variety of acute and chronic effects in humans. Cd accumulates in the human body, especially in the kidneys, resulting in kidney damage (renal tubular damage), which is a critical health effect. Other effects of Cd exposure are disturbances in calcium metabolism, hypercalciuria and the formation of kidney stones. High exposure to Cd can lead to lung cancer and prostate cancer; hence, poor quality water that may result in Cd toxicity has become a global concern. Thus, the aim of this study is to determine the concentration of Cd in underground water sources in western U.P. regions. Water samples were acidified to 1% with nitric acid and then stored in double-capped polyethylene bottles for further analysis by an atomic absorption spectrophotometer. After comparing the data to the WHO (2011) permissible limit, the study revealed that the concentration of Cd was higher than the regulatory threshold; therefore, the underground water system is seriously affected by Cd toxicity.     

Calculation of the flow into a lake from underground springs using sedimentation rates

The scope of this work is to quantify the upflows through the underground sources in the bottom of Lake Banyoles (NE-Iberia). The method applied uses the mean settling rate and the fraction of solids per unit of volume of the suspensions at the underground sources, and also the horizontal areas covered by these suspensions. The results obtained reveal that about 90% of the total underground inflow enters the lake through one of the sources. This result agrees with the total underground inflow calculated from the difference of the surface in and outflow of the lake. The behaviour of the suspensions at the underground sources was in a accordance with the theory used to developed the measuring method. Finally, the degree of turbulence in the upper part of the suspension and the importance of the transmissivity of the limestone layer next to the lake are discussed and are found to be negligible.     

宽甸县水中硼的背景浓度及污染现状分析

采集辽宁宽甸县各种水样51个,用ICP—MS分析硼含量。结果表明,宽甸县水中硼含量的背景值与世界水平相当,污染地区地表水和地下水硼含量的平均值分别是背景点的23．1和495．6倍。硼的开采和加工对水体产生了较严重的硼污染。     

Underground metabolism

All enzymes are able to use alternative substrates. When these are naturally occurring metabolites, an ‘underground reaction’ takes place. Examples are presented in which underground metabolism of this sort produces an observable phenotype. Although biological processes can be remakably accurate, evolution has selected error rates far from perfect. It is suggested here that a certain level of metabolic inaccuracy, in addition to saving energy, may also confer an evolutionary advantage, for example by providing metabolic plasticity. Since underground reactions are unpredictable from DNA sequence data, caution is in order when interpreting correlations between genetic disorders and pathological syndromes. BioEssays 20:181–186, 1998. © 1998 John Wiley & Sons, Inc.     

喀斯特裸坡产流产沙过程试验研究

运用可调坡度、地下孔(裂)隙度试验钢槽装填土石模拟喀斯特裸坡,采用人工模拟降雨的方法探索了喀斯特裸坡产流产沙过程。结果表明:降雨强度、坡度和地下孔(裂)隙度对喀斯特裸坡产流产沙均有明显的影响。(1)在30、50、80mm/h降雨强度下地表产流产沙存在临界降雨强度,临界降雨强度在50—80mm/h之间,地下孔(裂)隙产流量和产沙量均随降雨强度增大呈现先增大后减小的变化趋势,产流量随降雨强度变化顺序为503080mm/h,产沙量随降雨强度大小变化顺序为508030mm/h。(2)随着坡度增大,地下输沙模数减小,其大小随坡度变化的顺序为10°15°20°25°;同一降雨历程内,坡度越小,单位时间内的地下输沙模数减小量越大,其大小随坡度变化的顺序为10°15°20°25°。(3)地下孔(裂)隙度对地下产流产沙影响显著,地下孔(裂)隙度的增大使地下流失量增大。地下产流比重、产沙比重均随地下孔(裂)隙度的增大而增大,大小顺序均为1%3%5%。研究有助于深入了解喀斯特坡地土壤侵蚀机理,为喀斯特石漠化治理和生态修复提供理论依据。     

Genome‐wide adaptive evolution to underground stresses in subterranean mammals: Hypoxia adaption,immunity promotion,and sensory specialization

Life underground has provided remarkable examples of adaptive evolution in subterranean mammals; however, genome‐wide adaptive evolution to underground stresses still needs further research. There are approximately 250 species of subterranean mammals across three suborders and six families. These species not only inhabit hypoxic and dark burrows but also exhibit evolved adaptation to hypoxia, cancer resistance, and specialized sensory systems, making them an excellent model of evolution. The adaptive evolution of subterranean mammals has attracted great attention and needs further study. In the present study, phylogenetic analysis of 5,853 single‐copy orthologous gene families of five subterranean mammals (Nannospalax galili, Heterocephalus glaber, Fukomys damarensis, Condylura cristata, and Chrysochloris asiatica) showed that they formed fou distinct clusters. This result is consistent with the traditional systematics of these species. Furthermore, comparison of the high‐quality genomes of these five subterranean mammalian species led to the identification of the genomic signatures of adaptive evolution. Our results show that the five subterranean mammalian did not share positively selected genes but had similar functional enrichment categories, including hypoxia tolerance, immunity promotion, and sensory specialization, which adapted to the environment of underground stresses. Moreover, variations in soil hardness, climate, and lifestyles have resulted in different molecular mechanisms of adaptation to the hypoxic environment and different degrees of visual degradation. These results provide insights into the genome‐wide adaptive evolution to underground stresses in subterranean mammals, with special focus on the characteristics of hypoxia adaption, immunity promotion, and sensory specialization response to the life underground.     

Comparative Ecology of Rubus Species (Rosaceae) II. Reproductive Characteristics of Three Rubus Species, R. palmatus var. coptophyllus, R. microphyllus and R. crataegifolius

Abstract The reproductive characteristics of three Rubus species ( R. palmatus Thunberg var. coptophyllus (A. Gray) O. Kuntze, R. microphyllus L.f., and R. crataegifolius Bunge) were critically investigated using materials collected from the forest floor of an 85-year-old Hinoki ( Chamaecyparis obtusa ) plantation in central Honshu, Japan. The underground branching patterns of these species were also investigated at the nursery. R. microphyllus produced the largest number of fruits in the same cane size among the three species (164 fruits per cane of 300 cm³ in D₀2H). However, the largest number of seeds produced per cane was in R. crataegifolius , where the maximum seed number attained 74,500 per cane, which was twice as many as those of the other two species. There was no apparent difference in dry matter allocation to fruits in these species. The three species produced numerous suckers by underground branching, forming large clones. In the open site at the nursery, the number of suckers produced by underground branching increased exponentially. On the other hand, in natural populations occurring in closed sites, the number of suckers produced by underground branching in the three species was by contrast much smaller. Three Rubus species proved to possess similar perennation as well as reproductive strategies, although R. palmatus var. coptophyllus shows much lower seed production and slower sucker production than the other two species.     

Ectomycorrhizal characterization of an American chestnut <Emphasis Type="SmallCaps">(</Emphasis><Emphasis Type="Italic">Castanea dentata</Emphasis><Emphasis Type="SmallCaps">)</Emphasis>-dominated community in Western Wisconsin

Circa 1900, a farmer from the eastern US planted 11 American chestnut (Castanea dentata) seeds on a newly established farm near West Salem in western Wisconsin. These trees were very successful, producing a large stand of over 6,000 trees. Since this area is well outside the natural range of chestnut, these trees remained free from chestnut blight until 1987. In the West Salem stand, chestnuts are the dominant species of a mixed forest community, reminiscent of the chestnut–oak ecosystems of pre-1900 Appalachia. To identify putative mycorrhizal associates of chestnut in this unique forest, our approach was twofold: (1) an extensive fruiting body survey was conducted for four seasons that yielded approximately 100 putative mycorrhizal species and (2) a belowground molecular approach was used to generate DNA sequences of the internal transcribed spacer region from ectomycorrhizae. Unexpectedly, chestnut did not appear to be the dominant underground ectomycorrhizal-forming plant species. This study highlights the need to identify the plant host species when conducting belowground molecular-based surveys and provides preliminary identification of ectomycorrhizal fungi associated with a disjunct stand of American chestnut. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Climatic and hydrological aspects of the Hula restoration project

Drying the Hula marshes (northern Israel) in the 1950s caused changes in sub-surface hydrology that severely compromised agricultural sustainability of the Hula Valley peatlands. The complex dynamics between climatic and hydrological regimes produced widely fluctuating elevations in the water table, leading to deterioration of the peat soils through enhanced aerobic decomposition, wind erosion, and underground fires. The year-round intensive and diverse cropping systems used in 1960s were gradually replaced in the 1980s by extensive winter forage crops, leaving the peat uncropped and exposed to increased deterioration in the dry season. The Hula Restoration Project was initiated in 1993 to moderate some of these after-effects of the draining of the Hula marshes. The project includes a 90-km network of water-level regulating supply and drainage canals and a 100-ha lake and a barrier to underground water flow from the lake to cultivated areas. We followed changes in underground water levels for the five years before and the three years after re-flooding of the valley in May 1994. Prior to re- flooding, water tables in the area fluctuated 2–4 m annually, depending on location and microrelief and there was a strong north to south flow of water. After re-flooding the lake initially had a strong influence on water table elevation in the adjacent areas, which later stabilized. The underground barrier shifted the predominant water flow westward toward a north-south canal near the edge of the valley and then southward along the canal. The restoration project has been successful up to now, there are few underground fires since re-flooding, and all agricultural lands can be cultivated al year long.     

疏花水柏枝幼苗生物量与构件对模拟土壤地下水位变化的响应

通过模拟不同地下水位的方法,对疏花水柏枝（Myricaria laxiflora（Franch.）P.Y.Zhang et Y.J.Zhang）一年生幼苗在不同条件下地上与地下部生物量及构件的变化进行测定,分析幼苗生长对地下水位变化的响应。结果显示：随着地下水位的降低,疏花水柏枝幼苗的生长特征指标均呈先增加后减少的趋势,其中地上、地下部分生物量的最高值分别为0.0438、0.0100 g,最低值分别为0.0177、0.0026 g。幼苗地上部生物量在-10 cm处理水平最高;地下部生物量在-15 cm处理水平最高。幼苗直径、根表面积、株高、主根长度、根体积、一级枝数、二级枝数等指标也分别在-10 cm或-15 cm处理水平达到最高值。疏花水柏枝幼苗主要构件的生长与地下水位的变化存在显著相关性。主成分分析结果表明,幼苗的地下部分更容易受到土壤地下水位变化的影响,幼苗性状症候群随地下水位的变化而发生移动,说明该物种幼苗在不同地下水位时的生长投资策略具有较大差异。     

Dietary reconstruction of Spy I using dental microwear texture analysis

Spy I from the Meuse River Basin of Belgium is among the most recent Neandertals. This adult lived at the terminus of Marine Isotope Stage (MIS) 3 in cold steppe environments at the northern edge of the habitable zone for Neandertals where plants were relatively scarce. The dietary proclivities of Spy I are reconstructed using dental microwear texture analysis and compared to 33 Neandertals from western Eurasia, MIS 5 to MIS 3. Spy I has an elevated enamel surface complexity suggesting the consumption of course dietary items such as wild seeds, acorns, nuts, and underground storage organs laden with particles of grit. Unlike the young and old individuals from Hortus with low values for anisotropy, Spy I is closest to the adults from this site suggesting a common pattern of masticatory behavior typified this life cycle stage. Like many other Neandertals, Spy I probably consumed plant foods at appreciable levels, some of which were hard and brittle or poorly processed.     

Conservation Implications of Spatiotemporal Variation in the Terrestrial Ecology of Western Spadefoots

Conservation of species reliant on ephemeral resources can be especially challenging in the face of a changing climate. Western spadefoots (Spea hammondii) are small burrowing anurans that breed in ephemeral pools, but adults spend the majority of their lives underground in adjacent terrestrial habitat. Western spadefoots are of conservation concern throughout their range because of habitat loss, but little is known about the activity patterns and ecology of their terrestrial life stage. We conducted a radio-telemetry study of adult western spadefoots at 2 sites in southern California, USA, from December 2018 to November 2019 to characterize their survival, behavior, and movements from breeding through aestivation to refine conservation and management for the species. Western spadefoot survival varied seasonally, with risk of mortality higher in the active season than during aestivation. The probability of movement between successive observations was higher during the winter and spring and when atmospheric moisture was high and soil water content at 10-cm depth was low. The amount of rain between observations had the strongest effect on the probability of movement between observations; for every 20 mm of rainfall between observations, western spadefoots were 2.4 times more likely to move. When movements occurred, movement rates were highest when both relative humidity and soil water content at 10-cm depth were high. The conditions under which western spadefoots were likely active on the surface, likely to have moved, and moved at the highest rates are conditions that reduce the risk of desiccation of surface-active spadefoots. Western spadefoot home range areas varied between study sites and were mostly <1 ha, although 1 individual's home range area was >6 ha. Western spadefoots rapidly dispersed from the breeding pools, and asymptotic distances from the breeding pool were generally reached by June. The asymptotic distance from the breeding pool varied between sites, with the 95th percentile of the posterior predictive distribution reaching 486 m at 1 site and 187 m at the other. Western spadefoots did not select most habitat components disproportionately to their availability, but at Crystal Cove State Park, they avoided most evaluated vegetation types (graminoids, forbs, and shrubs). Spatial variation was evident in most evaluated western spadefoot behaviors; context-dependent behavior suggests that site-specific management is likely necessary for western spadefoots. Furthermore, comparison with an earlier study of western spadefoots at Crystal Cove State Park indicated substantial temporal variation in western spadefoot behavior. Therefore, basing management decisions on short-term studies might fail to meet conservation objectives. Better understanding the influences of spatial context and climatic variation on western spadefoot behavior will improve conservation efforts for this species. © 2021 This article is a U.S. Government work and is in the public domain in the USA. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

Genetic diversity and divergence among freshwater mussel (Anodonta) populations in the Bonneville Basin of Utah

Populations of the freshwater mussel genus Anodonta appear to be in a state of rapid decline in western North America, following a trend that unfortunately seems to be prevalent among these animals (Mollusca: Unionoida). Here we describe the patterns of molecular divergence and diversity among Anodonta populations in the Bonneville Basin, a large sub-basin of the Great Basin in western North America. Using amplified fragment length polymorphism (AFLP) analysis, we found a striking lack of nuclear diversity within some of these populations, along with a high degree of structuring among populations (FST = 0.61), suggesting post-Pleistocene isolation, due either to a long-term loss of hydrologic connectivity among populations or to more recent fish introductions. We also found evidence of recent hybridization in one of these populations, possibly mediated by fish-stocking practices. Using mitochondrial sequence data, we compared the Bonneville Basin populations to Anodonta in several other drainages in western North America. We found a general lack of resolution in these phylogenetic reconstructions, although there was a tendency for the Bonneville Basin Anodonta (tentatively A. californiensis) to cluster with A. oregonensis from the adjacent Lahontan Basin in Nevada. We recommend further investigation of anthropogenic factors that may be contributing to the decline of western Anodonta and a broad-scale analysis and synthesis of genetic and morphological variation among Anodonta in western North America.     

中国草地地下生物量研究进展

在草地生态学研究中,草地地下生物量的研究是必不可少的环节,地下部分无论是生理功能还是对草地植被碳蓄积贡献都具有举足轻重的地位。本文综述了中国当前草地地下生物量的研究方法和内容,包括草地地下生物量的测定方法,草地地下生物量的垂直空间分布规律,年度季节动态,地下地上生物量比值关系及动态,以及影响草地地下生物量的环境因子和人为因子。最后提出了我国草地地下生物量研究面临的主要问题及研究的发展趋势。