Multiplex PCR for Assessment of Tetracycline Resistance (tet) Genes in Antibiotic-Resistant Soil Bacteria and the Ecological Implications

Antibiotics are becoming increasingly prevalent in bacterial communities due to clinical and agricultural misuse and overuse in their environment. As exposure increases, so does the incidence of microbial resistance. Such is the case with bacterial resistance to tetracyclines, a phenotype often acquired through the horizontal gene transfer of tet genes between bacteria. The objective of this project was to analyze the bacterial diversity of tet resistance genes in soil from Miami-Dade County. Bacterial isolates were Gram-stained and the Kirby-Bauer antibiotic disk diffusion test was performed to determine each bacterium’s degree of resistance. The 16S rRNA gene from antibiotic-resistant isolates was amplified by PCR and sequenced to identify the isolates. All isolates’ tet genes were amplified by multiplex PCR, sequenced, and compared. Among eight isolates, three distinct species were positively identified based on their 16S rRNA sequences and four distinct tet genes were identified, though all tested susceptible to tetracycline via the Kirby-Bauer test. This project clarifies some aspects of the ecology of antibiotic resistance genes, their natural ecological function and the potential for the expansion of intrinsic multi-antibiotic resistance into new ecosystems and/or hosts.

The short-term effects of a routine poisoning campaign on the movements and detectability of a social top-predator

Top-predators can be important components of resilient ecosystems, but they are still controlled in many places to mitigate a variety of economic, environmental and/or social impacts. Lethal control is often achieved through the broad-scale application of poisoned baits. Understanding the direct and indirect effects of such lethal control on subsequent movements and behaviour of survivors is an important pre-requisite for interpreting the efficacy and ecological outcomes of top-predator control. In this study, we use GPS tracking collars to investigate the fine-scale and short-term movements of dingoes (Canis lupus dingo and other wild dogs) in response to a routine poison-baiting program as an example of how a common, social top-predator can respond (behaviourally) to moderate levels of population reduction. We found no consistent control-induced differences in home range size or location, daily distance travelled, speed of travel, temporal activity patterns or road/trail usage for the seven surviving dingoes we monitored immediately before and after a typical lethal control event. These data suggest that the spatial behaviour of surviving dingoes was not altered in ways likely to affect their detectability, and if control-induced changes in dingoes' ecological function did occur, these may not be related to altered spatial behaviour or movement patterns.

Impacts on nontarget avian species from aerial meat baiting for feral pigs

Bait containing sodium fluoroacetate (1080) is widely used for the routine control of feral pigs in Australia. In Queensland, meat baits are popular in western and northern pastoral areas where they are readily accepted by feral pigs and can be distributed aerially. Field studies have indicated some levels of interference and consumption of baits by nontarget species and, based on toxicity data and the 1080 content of baits, many nontarget species (particularly birds and varanids) are potentially at risk through primary poisoning. While occasional deaths of species have been recorded, it remains unclear whether the level of mortality is sufficient to threaten the viability or ecological function of species. A series of field trials at Culgoa National Park in south-western Queensland was conducted to determine the effect of broadscale aerial baiting (1.7 baits per km2) on the density of nontarget avian species that may consume baits. Counts of susceptible bird species were conducted prior to and following aerial baiting, and on three nearby unbaited properties, in May and November 2011, and May 2012. A sample of baits was monitored with remote cameras in the November 2011 and May 2012 trials. Over the three baiting campaigns, there was no evidence of a population-level decline among the seven avian nontarget species that were monitored. Thirty per cent and 15% of baits monitored by remote cameras in the November 2011 and May 2012 trials were sampled by birds, varanids or other reptiles. These results support the continued use of 1080 meat baits for feral pig management in western Queensland and similar environs.

The (Non)Effects of Lethal Population Control on the Diet of Australian Dingoes

Top-predators contribute to ecosystem resilience, yet individuals or populations are often subject to lethal control to protect livestock, managed game or humans from predation. Such management actions sometimes attract concern that lethal control might affect top-predator function in ways ultimately detrimental to biodiversity conservation. The primary function of a predator is predation, which is often investigated by assessing their diet. We therefore use data on prey remains found in 4,298 Australian dingo scats systematically collected from three arid sites over a four year period to experimentally assess the effects of repeated broad-scale poison-baiting programs on dingo diet. Indices of dingo dietary diversity and similarity were either identical or near-identical in baited and adjacent unbaited treatment areas in each case, demonstrating no control-induced change to dingo diets. Associated studies on dingoes' movement behaviour and interactions with sympatric mesopredators were similarly unaffected by poison-baiting. These results indicate that mid-sized top-predators with flexible and generalist diets (such as dingoes) may be resilient to ongoing and moderate levels of population control without substantial alteration of their diets and other related aspects of their ecological function.

Seed dispersal in changing landscapes

A growing understanding of the ecology of seed dispersal has so far had little influence on conservation practice, while the needs of conservation practice have had little influence on seed dispersal research. Yet seed dispersal interacts decisively with the major drivers of biodiversity change in the 21st century: habitat fragmentation, overharvesting, biological invasions, and climate change. We synthesize current knowledge of the effects these drivers have on seed dispersal to identify research gaps and to show how this information can be used to improve conservation management. The drivers, either individually, or in combination, have changed the quantity, species composition, and spatial pattern of dispersed seeds in the majority of ecosystems worldwide, with inevitable consequences for species survival in a rapidly changing world. The natural history of seed dispersal is now well-understood in a range of landscapes worldwide. Only a few generalizations that have emerged are directly applicable to conservation management, however, because they are frequently confounded by site-specific and species-specific variation. Potentially synergistic interactions between disturbances are likely to exacerbate the negative impacts, but these are rarely investigated. We recommend that the conservation status of functionally unique dispersers be revised and that the conservation target for key seed dispersers should be a population size that maintains their ecological function, rather than merely the minimum viable population. Based on our analysis of conservation needs, seed dispersal research should be carried out at larger spatial scales in heterogenous landscapes, examining the simultaneous impacts of multiple drivers on community-wide seed dispersal networks. (C) 2011 Elsevier Ltd. All rights reserved.

Literature review for a resource characterization of Cape Romain National Wildlife Refuge

Through research aimed at understanding the coastal environment, surveys designed to help manage the resource, and national programs to monitor environmental condition, we see a picture of a dynamic ecosystem that is Cape Romain National Wildlife Refuge (CRNWR). Currently, there are efforts underway to protect threatened species; monitor fish populations; and quantify the biological, physical, and chemical characteristics of this environment. The potential impacts to this system are just now being understood as ecological responses to human modification are observed and explained. As a starting point, this document compiles existing information about Cape Romain NWR in five topic areas and addresses the potential impacts to the Refuge. This review is intended to serve as a stepping stone to developing a research agenda in support of management of the Refuge. There are various sources of information on which to build a framework for monitoring conditions and detecting change to this environment. For instance, information on basic ecological function in estuarine environments has evolved over several decades. Long-term surveys of Southeast fisheries exist, as well as shellfish and sediment contaminants data from estuaries. Environmental monitoring and biological surveys at the Refuge continue. Recently, studies that examine the impacts to similar coastal habitats have been undertaken. This document puts past studies and ongoing work in context for Refuge managers and researchers. This report recommends that the next phase of this resource characterization focus on: • compiling relevant tabular and spatial data, as identified here, into a Geographic Information System (GIS) framework • assessing the abundance and diversity of fisheries utilizing CRNWR • delineating additional data layers, such as intertidal habitats and subtidal clam beds, from low-level aerial photography, hard copy maps, and other sources • continued inventories of plant and animal species dependent on the Refuge • monitoring physical and chemical environmental parameters using the methodology employed at National Estuarine Research Reserve System (NERRS) and other coastal sites, where appropriate • further definition of the potential risks to the Refuge and preparing responses to likely impacts.

辽宁省生态系统评价与生态功能分区研究

生态系统评价是为了向决策者提供生态系统管理信，息而对生态系统结构、功能进行分析，并根据其变化趋势及驱动力提出相应措施的综合研究过程。生态功能分区是依据生态系统胁迫过程与效应、生态环境质量、敏感性和生态系统服务功能重要性等特征空间分异规律而进行的地理空间分区，目的是辨析区域生态环境问题与生态环境脆弱区和良好区，明确优先保护的生态系统和地区，为生态保护与建设、产业结构调整与优化及区域生态系统分区管理提供科学依据。本研究以辽宁省域生态系统为对象，在生态环境调查的基础上，分析了生态环境状况及变化趋势，进行了生态环境质量、敏感性和生态系统服务功能重要性评价，辨析了存在的生态环境问题及驱动力，明确了生态环境质量、敏感性和生态系统服务功能重要性空间分布格局，然后对辽宁省进行了生态功能区划分，并指出了各功能区生态保护与建设的重点和措施以及产业结构调整与优化的对策和方向研究结果表明，在经济和人口增长的长期胁迫作用下，辽宁省生态环境问题依然严峻，主要表现为：土地退化，地表水污染严重，森林质量下降和功能减弱，草地减少与退化并存，天然湿地萎缩，滩涂和海岸带生境恶化，生物多样性面临威胁，农业面源污染凸显，生态系统抗干扰能力下降，生态灾害加剧。全省生态环境质量超过2／3属于一般以下水平，其中优级面积仅占12.56％，良好级面积占18.71％，主要分布在东部及东南部；一般级面积占34.25％，主要分布在中部、北部和南部；较差级面积占34.48％，主要分布在西部及西北部。全省县级市及县有44个，其中生态环境质量为优的仅有4个市县，占总县数的9.09％；生态环境质量为良的有7个市县，占总县数的15.91％；生态环境质量一般的有19个市县，占总县数的43.18％，生态环境质量较差的有14个市县，占总县数的31.82％。全省处于轻度至高度敏感区域。高度敏感区占34.00％，主要分布在辽东山地丘陵、辽东半岛、辽西低山丘陵、辽西北、柳绕地区和大洼县。辽东山地丘陵、辽东半岛和辽西低山丘陵主要是土壤侵蚀高度敏感。辽西北和柳绕地区主要是土地沙漠化高度敏感。大洼县是土壤盐渍化高度敏感。中度敏感区占能．66％，与高度敏感区相间分布。轻度敏感区占3.34％，零星分布在辽东，在辽西和辽河平原也有少量分布。全省生态服务功能均处于比较重要以上。极重要地区占60.66％，基本分布在辽东、辽西和辽河平原的北部与盘锦滨海地区，辽东主要为水源涵养、生物多样性保护、土壤保持、营养物质保持，辽西主要为土壤保持、生物多样性保护、水源涵养、营养物质保持，辽北主要为土壤保持，盘锦滨海地区主要为生物多样性保护。中等重要地区占37.01%，基本分布在辽河平原，在辽东、辽西也有分布，辽河平原主要为土壤保持、水源涵养，沙漠化控制，辽东和辽西主要为土壤保持，辽西北为沙漠化控制。其它地区为比较重要地区，仅占2.33％，主要分布在辽东和辽河平原，在辽西也有少量分布，主要为土壤保持。在生态系统评价的基础上，首先根据地貌和气候划分出4个生态区，即辽东山地丘陵温带湿润半湿润生态区、辽河平原温带半湿润生态区、辽西低山丘陵温带半湿润生态区、辽南环黄渤海海岸带生态区。在明确生态区的基础上，依据生态系统类型与过程的完整性，以及生态服务功能类型的一致性，划分出21个生态亚区。依据生态环境质量、敏感性及生态服务功能重要性等的一致性，进一步划分出52个生态功能区。

植物化感作用与生物多样性

本文简要地阐释了化感作用的含义、基本特征以及作用机制,并结合生物多样性理论,综述了化感作用研究中化感物种的多样性、化感物质的多样性及其释放途径的多样性,具体讨论了化感作用对物种多样性、遗传多样性及生态系统多样性中的种群生态、协同进化、土壤生境、生态系统功能和生物入侵等方面的可能影响。文中提出了化感作用的利用、管理应与生物多样性保护相统一的看法,并指出对化感作用与生物多样性的关系以及相互影响机制进行本质的探索,特别是对植物化感作用的生态服务功能与价值评估与探讨,可为保护生物学和系统生态学提供理论基础,这也是今后工作开展的一个重要方向。

生物土壤结皮的生态功能

Biological soil crust exists in desertification-prone areas.This paper focuses on ecological function of biological soil crust,including water relations,soil stabilization,carbon and nitrogen fixation,albedo and effects on vascular plants.Some preliminary suggestions are given for further understanding the relationship between biological soil crust and revegetation of degraded ecosystem in desertification-prone areas in Northwestern China.

Growth characters and photosynthetic capacity of Gracilaria lemaneiformis as a biofilter in a shellfish farming area in Sanggou Bay, China

Experiments on growth characters and ecological functions of the macroalgae Gracilaria lemaneiformis, collected from south China, were conducted in polyculture areas of kelp and filter-feeding bivalve in Sanggou Bay in Weihai City, Shandong, in north China from May 2002 to May 2003. The results of 116 days cultivation showed that the average wet weight of alga increased 89 times from 0.1 to 8.9 kg rope(-1), with an average specific growth rate ( based on wet weight) of 3.95% per day. The most favorable water layer for its growth was 1.0 - 1.8 m below the surface in July and August, with an average specific growth rate of 8.2% per day in 30-day experiments. Photosynthetic activity changed seasonally, with an average of 7.3 mg O-2 g dw(-1) h(-1). The maximum rate (14.4 mg O-2 g dw(-1) h(-1)) was recorded in July, or 19.3 mg CO2 g dw(-1) h(-1), while the minimum (0.40 mg CO2 g dw(-1) h(-1)) was in April. This study indicated that the culture of G. lemaneiformis is an effective way to improve water quality where scallops are cultivated intensively.

iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework

Ocean biogeochemistry (OBGC) models span a wide variety of complexities, including highly simplified nutrient-restoring schemes, nutrient–phytoplankton–zooplankton–detritus (NPZD) models that crudely represent the marine biota, models that represent a broader trophic structure by grouping organisms as plankton functional types (PFTs) based on their biogeochemical role (dynamic green ocean models) and ecosystem models that group organisms by ecological function and trait. OBGC models are now integral components of Earth system models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here we present an intercomparison of six OBGC models that were candidates for implementation within the next UK Earth system model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the ocean general circulation model Nucleus for European Modelling of the Ocean (NEMO) and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform all other models across all metrics. Nonetheless, the simpler models are broadly closer to observations across a number of fields and thus offer a high-efficiency option for ESMs that prioritise high-resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low-resolution climate dynamics and high-complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry–climate interactions.

Qu’est-ce que le bien des écosystèmes? Fondements philosophiques des notions de fonction écologique et de santé écosystémique

L’objectif de cette thèse est de proposer une caractérisation du bien propre des touts écologiques, comme les communautés biotiques et les écosystèmes, dont peut être dérivée une notion de ce qui est bon pour eux. Ceci vise à défendre les deux principales approches holistes en éthique de l’environnement, c’est-à-dire l’approche pragmatiste défendue par Bryan G. Norton et l’approche écocentriste défendue par J. Baird Callicott, contre certaines objections ayant été soulevées contre elles, faisant valoir l’impossibilité pour les écosystèmes d’avoir un bien propre. Cette thèse répond à ces objections en mobilisant plusieurs ressources théoriques issues de la philosophie de la biologie et de la méta-éthique. Ces ressources sont notamment celles fournies par les discussions sur les notions de fonction et de santé en philosophie de la biologie, celles fournies par les conceptions néo-aristotéliciennes de la normativité en méta-éthique, et celles offertes par les discussions de philosophie de l’écologie sur le holisme et le réductionnisme, sur l’idée d’équilibre de la nature, et sur le concept de santé écosystémique. Cette thèse mobilise ces ressources afin d’élaborer les fondements philosophiques des notions de fonction écologique et de santé écosystémique, desquelles est dérivée une caractérisation du bien propre des écosystèmes.

Future landscapes in South-eastern Australia : the role of protected areas and biolinks in adaptation to climate change

The extent and rapidity of global climate change is the major novel threatening process to biodiversity in the 21 st century. Globally, numerous studies suggest movement of biota to higher latitudes and altitudes with increasing empirical -evidence emerging. As biota responds to the direct and consequent effects of climate change the potential to profoundly affect natural systems (including the reserve system) of south-eastern Australia is becoming evident. Climate change is projected to accelerate major environmental drivers such as drought, fire and flood regimes. Is the reserve system sufficient for biodiversity conservation under a changing climate? Australia is topographically flat, biologically mega-diverse with high species endemism, and has the driest and most variable climate of any inhabited continent. Whilst the north-south orientation and aftitude gradient of eastern Australia's forests and woodlands provides some resilience to projected climatic change, this has been eroded since European settlement, particularly in the cool-moist Bassian zone of the south-east. Following settlement, massive land-use change for agriculture and forestry caused widespread loss and fragmentation of habitats; becoming geriatric in agricultural landscapes and artificially young in forests. The reserve system persists as an archipelago of ecological islands surrounded by land uses of varying compatibility with conservation and vulnerable to global warming. The capacity for biota to adapt is limited by habitat availability. The extinction risk is exacerbated. Re-examination of earlier analysis of ecological connectivity through biolink zones confirms biolinks as an appropriate risk management response within a broader suite of measures. Areas not currently in the reserve system may be critical to the value and ecological function of biological assets of the reserve system as these assets change. Ecological need and the rise of ecosystem services, combined with changing socio-economic drivers of land-use and social values that supported the expansion of the reserve system, all suggest biolink zones represent a new, necessary and viable multi-functional landscape. This paper explores some of the key ecological elements for restoration within biolink zones (and landscapes at large) particularly through currently agricultural landscapes.

Top predators as biodiversity regulators : the dingo Canis lupus dingo as a case study

Top-order predators often have positive effects on biological diversity owing to their key functional roles in regulating trophic cascades and other ecological processes. Their loss has been identified as a major factor contributing to the decline of biodiversity in both aquatic and terrestrial systems. Consequently, restoring and maintaining the ecological function of top predators is a critical global imperative. Here we review studies of the ecological effects of the dingo Canis lupus dingo, Australia's largest land predator, using this as a case study to explore the influence of a top predator on biodiversity at a continental scale. The dingo was introduced to Australia by people at least 3500 years ago and has an ambiguous status owing to its brief history on the continent, its adverse impacts on livestock production and its role as an ecosystem architect. A large body of research now indicates that dingoes regulate ecological cascades, particularly in arid Australia, and that the removal of dingoes results in an increase in the abundances and impacts of herbivores and invasive mesopredators, most notably the red fox Vulpes vulpes. The loss of dingoes has been linked to widespread losses of small and medium-sized native mammals, the depletion of plant biomass due to the effects of irrupting herbivore populations and increased predation rates by red foxes. We outline a suite of conceptual models to describe the effects of dingoes on vertebrate populations across different Australian environments. Finally, we discuss key issues that require consideration or warrant research before the ecological effects of dingoes can be incorporated formally into biodiversity conservation programs.

Are we predicting the actual or apparent distribution of temperate marine fishes?

Planning for resilience is the focus of many marine conservation programs and initiatives. These efforts aim to inform conservation strategies for marine regions to ensure they have inbuilt capacity to retain biological diversity and ecological function in the face of global environmental change – particularly changes in climate and resource exploitation. In the absence of direct biological and ecological information for many marine species, scientists are increasingly using spatially-explicit, predictive-modeling approaches. Through the improved access to multibeam sonar and underwater video technology these models provide spatial predictions of the most suitable regions for an organism at resolutions previously not possible. However, sensible-looking, well-performing models can provide very different predictions of distribution depending on which occurrence dataset is used. To examine this, we construct species distribution models for nine temperate marine sedentary fishes for a 25.7 km2 study region off the coast of southeastern Australia. We use generalized linear model (GLM), generalized additive model (GAM) and maximum entropy (MAXENT) to build models based on co-located occurrence datasets derived from two underwater video methods (i.e. baited and towed video) and fine-scale multibeam sonar based seafloor habitat variables. Overall, this study found that the choice of modeling approach did not considerably influence the prediction of distributions based on the same occurrence dataset. However, greater dissimilarity between model predictions was observed across the nine fish taxa when the two occurrence datasets were compared (relative to models based on the same dataset). Based on these results it is difficult to draw any general trends in regards to which video method provides more reliable occurrence datasets. Nonetheless, we suggest predictions reflecting the species apparent distribution (i.e. a combination of species distribution and the probability of detecting it). Consequently, we also encourage researchers and marine managers to carefully interpret model predictions.