太湖梅梁湾水域蓝藻水华前与水华末期细菌群落结构的变化

通过16S rRNA克隆文库研究了太湖梅梁湾2004年3月和9月表层水样中细菌组成的变化,发现在蓝藻水华前与水华末期的菌群结构存在差异,特别是最优势的细菌发生了很大变化.3月水样中的克隆子主要与Bacteroidetes(42.7%)、β-Proteobacteria(18.4%)、α-Proteobacteria(16.5%)和Actinobacteria(16.5%)相关,9月水样中的克隆子主要与Cyanobacteria(28.8%)、β-Proteobacteria(25.0%)、Actinobacteria(17.3%)和α-Proteobacteria(15.4%)相关.此外,在水华末期(9月)的细菌组成更为多样性,有11个类群;而未发生水华时(3月)的细菌组成只有7个类群.同相关研究比较发现,α、β-Proteobacteria,Actinobacteria均为太湖中的常见菌群,其分布较为广泛;而γ-Proteobacteria和Firmicutes多出现于太湖的沉积物中,在水体中较少出现;属于Bacteroidetes这一类群的浮游细菌在湖水中很丰富.所研究水域中发现的很多细菌的16SrRNA基因与出现在许多不同的淡水生境,包括国外贫营养湖、中营养湖和富营养湖中细菌的系统关系密切,还发现大量源于长江的克隆子,很少有与海洋中细菌相似的序列(除Bacteroidetes门的成员外).图2表3参21     

隐球酵母Zwy-2-3循环利用油脂发酵废弃细胞产油

为提高资源利用效率,降低微生物油脂发酵成本,解决微生物油脂发酵中废弃酵母细胞和发酵废液处理排放的问题,研究隐球酵母(Cryptococcus podzolicus)Zwy-2-3利用栎类淀粉发酵产油情况,并探讨发酵废液和废弃酵母细胞酶解液作为氮源的循环利用.结果显示,以葡萄糖60 g/L和总氮0.18 g/L的废弃酵母细胞酶解液发酵时,循环3次其油脂产量分别达到6.79 g/L、6.66 g/L、6.72 g/L,均高于对照组;而将发酵废液回收用作废弃酵母细胞酶解的缓冲液时,其生物量、油脂产量同对照组相当;将该方法应用于栎类淀粉水解液同步糖化发酵产油脂的实验,循环3次后其生物量、油脂产量分别为13.04 g/L、7.13 g/L,比对照组提高了9.85%、10.03%,且3次循环的油脂含量较为稳定.油脂组分分析结果显示,菌株Zwy-2-3利用栎类淀粉同步糖化和废弃细胞循环酶解液发酵生产的微生物油脂不饱和脂肪酸的含量达到93%以上,与植物油组成相似.综上,酶解废弃酵母细胞可有效应用于酵母产油发酵,可为非粮淀粉生产的微生物油脂应用于生物柴油生产奠定基础.     

不同C/N值下亚硝酸盐氧化菌和异养菌混合体系的微生物多样性

采用PCR-RFLP技术研究了不同C/N比下亚硝酸盐氧化菌及异养菌混合体系的微牛物多样性,并探讨了微生物菌群结构与其功能(硝化件能)的关系.C/N=0时,混合体系主要由自养菌和寡营养菌(85.1%)组成,包括亚硝酸盐氧化菌(NOB)、拟杆菌门、α-变形菌纲、浮霉菌门和绿色非硫细菌中的一些菌株.C/N=0.44时,混合体系中的自养菌减少,异养菌(主要是γ-变形菌纲的成员)大量出现.C/N=8.82时,γ-变形菌纲的菌株尤其是反硝化菌Pseudomonas sp.占主导(93.8%),与此同时,随着C/N升高,该混合体系的硝化性能也由专一的亚硝酸盐氧化过程转变为同时硝化反硝化过程.微生物菌群结构的转变较好地解释了其硝化性能的改变.本研究揭示了微生物菌群结构与其功能的内在联系,同时表明PCR-RFLP技术与化学分析相结合是研究微生物菌群结构与功能的有力工具.图3表2参13     

秦皇岛近海养殖对潮间带微生物群落多样性的影响

潮间带微生物群落在驱动海岸带生态系统物质循环和能量流动中具有重要作用,近海养殖造成的环境问题日益凸显,但其对潮间带微生物群落结构的影响还缺乏研究。采用变性梯度凝胶电泳（DGGE）和限制性片段长度多态性（RFLP）的分子生物学技术,研究秦皇岛养殖区与旅游区潮间带沉积物中微生物多样性的差异,分析养殖区微生物的16S rRNA基因文库的组成特征。结果表明：养殖区的微生物群落结构与旅游区形成较大的差异,DGGE图谱中养殖区的特有条带主要集中于γ-变形菌纲（γ-proteobacteria）,还分布于α-变形菌纲（α-proteobacteria）,拟杆菌门（Bacteroidetes）,放线菌门（Actinobacteria）和厚壁菌门（Firmicutes）。影响潮间带微生物的群落结构的主要环境因子包括温度、盐度、pH和NO3-浓度,影响率达55.2%。对差异最大的洋河大桥南养殖区（Q1站）的微生物样品建立克隆文库分析群落结构,变形菌门（Proteobacteria）为优势菌群,占总群落的60%,其中γ-变形菌纲是主要存在的微生物纲,其余菌群包括放线菌门、拟杆菌门、蓝藻菌门（Cyanobacteria）和疣微菌门（Verrucomicrobia）的微生物。养殖区海岸带微生物群落中出现了与环境污染和赤潮密切相关的菌群,如拟杆菌门、肠杆菌属（Enterobacteriaceae）和α-变形细菌红细菌目（Roseovarius）的微生物。     

南极中山站排污口土壤中微生物群落的DGGE分析

以南极中山站排污口土壤为研究对象,提取样品中微生物宏基因组DNA,用变性梯度凝胶电泳(DGGE)对宏基因组DNA中的16S rRNA基因V3可变区进行分析,测定了31个不同条带所代表的序列.比较结果显示,排污口土壤样品与相同生境对照样品中的微生物类群组成均以CFB (Cytophaga-Flexibacteria-Bacteroides)类群和γ-变形菌纲(γ-Proteobacteria)为主,另外还有少量的α-, β-, δ-变形菌纲,和一些原核的藻类和革兰氏阳性细菌(G ). 但在排污口土壤样品中检出了传染性微生物毛球菌属(Trichococcus)和狡诈菌属(Dolosigranulum),以及丰富的小球藻(Chlorella),说明污水的排放已经对该地微生物群落造成明显的影响.     

祁连山冻土区土壤活动层与冻土层中甲烷代谢微生物群落结构特征

冻土土壤中的甲烷代谢微生物可氧化或产生甲烷,影响着甲烷所参与的碳循环过程,对于全球温室气体的释放和调节具有重要的作用.对祁连山冻土区土壤活动层与冻土层中的甲烷代谢微生物产甲烷菌(Methanogens)和甲烷氧化菌(Methanotrophs)的群落结构组成进行研究.通过对产甲烷菌的mcrA基因和甲烷氧化菌的pmoA基因进行PCR扩增,分别构建其基因克隆文库,并通过序列同源比对进行系统发育分析和多样性分析.结果显示:冻土土壤活动层中的产甲烷菌包括Rice cluster Ⅰ、Methanosarcinaceae、Methanomicrobiales、Methanosaetaceae、Methanobacteriaceae五种类型,而在土壤冻土层则包括了Rice cluster Ⅰ、Methanosarcinaceae、Methanobacteriaceae三种类型.土壤活动层的甲烷氧化菌由隶属于α-Proteobacteria(Type Ⅱ)的Methylocystis和隶属于γ-Proteobacteria(Type Ⅰ)的Methylobacter两种类型群体组成,而土壤冻土层中则只包括了Methylocystis这一种类型.由此可见,冻土土壤活动层与冻土层中的甲烷代谢微生物群落结构存在一定的差异.     

室温条件下油藏采出液微生物群落结构稳定性

获得准确的油藏微生物群落信息是开展油藏微生物工业化应用的重要前提.为了解油藏采出液脱离油藏环境后微生物群落结构的变化以及一个时间点的单次取样的代表性,利用目前最先进的高通量测序技术,对胜利油田油藏采出液室温放置5 d内的微生物群落结构以及连续5 d独立取样的同一油井水样间的微生物群落结构开展研究.结果显示,室内放置0-5 d过程中,细菌和古菌群落结构中的优势菌群没有发生明显改变,细菌的优势菌为热硫还原杆菌属(Thermodesulforhabdus)、无色杆菌属(Achromobacter)、沙雷氏菌(Serratia)以及一些未分类的细菌,古菌的优势菌为古生球菌属(Archaeoglobus)、产甲烷球菌属(Methanococcus)和甲烷鬃毛菌属(Methanosaeta).但是细菌和古菌的多样性存在逐渐降低的趋势,其中古菌多样性的变化比细菌更为明显.同时研究也证实同一口油井连续5 d独立取样的样品间,细菌和古菌群落结构中的优势菌群也没有发生较大的变化,与室内放置样品的优势菌属一致,多样性分析同样发现油藏内不同时间点古菌多样性的波动较细菌的大.本研究说明油藏采出液室温放置短期内优势菌群结构具有稳定性,一次取样的油水井样品具有阶段代表性,这可为高通量测序技术在油藏微生物群落结构解析中的应用提供重要理论支撑.     

低温纤维素降解菌的分离与鉴定

对内蒙古部分地区土壤中低温降解纤维素的微生物进行研究,以期获得一些高酶活的低温纤维素酶产生菌.采用纯培养的方法,在10℃下培养获得纯培养物.以细菌16S rDNA通用引物PCR扩增后进行序列同源性比对确定种属.以DNS法测定纤维素酶活性,并对酶活较高的菌株进行产酶条件的优化.结果共分离得到55株可低温降解纤维素的菌株,16S rDNA序列分析表明它们分别属于γ-变形菌纲(γ-Proteobacteria)、硬壁菌门(Firmicutes)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)以及β-变形菌纲(β-Proteobacteria).该55株菌的纤维素酶活性均在22℃下最高.其中菌株CF11在10℃下的酶活在分离得到的55株细菌中最高.通过优化,菌株CF11产纤维素酶的最佳条件初步确定为pH值为6.5,培养时间为10 d,并且是以酵母提取物作为氮源,其纤维素酶活为58.091 IU.因此菌株CF11是一株极具开发潜力的低温纤维素酶产生菌.     

油井采出液中硝酸盐还原菌的分离培养及对硫酸盐还原的抑制

采用油井采出液培养基和加入无机盐成分的改良油井采出液培养基,对大庆油田萨北过渡带油井采出液中的细菌进行分离培养及初步鉴定,比较了两种情况下培养出的具有硝酸盐和/或亚硝酸盐还原,以及/或反硝化能力菌群结构的差异.利用采出液培养基培养出一组新的微生物菌株,并且分离的硝酸盐和/或亚硝酸盐还原菌,以及/或反硝化细菌(Nitrate/nitrite reducing bacteria,denitrifying bacteria,NRDB)比例明显高于无机盐-采出液培养基;但培养基中无机盐成分的添加,提高了可培养NRDB的群落生物多样性.仅仅向油井采出液中直接投加硝酸盐作为电子受体,对其中硝酸盐还原、亚硝酸盐还原和反硝化微生物(NRDB)的激活作用以及产抑制硫化物产生的能力有限,而同时加入分离自采出液的NRDB和硝酸盐则对硫酸盐还原菌(SRB)的生长和产硫化物活性都产生了明显的抑制.但是NRDB与硝酸盐同时投加对不同SRB的抑制效果并不相同,导致了SRB群落结构的变化.图5表2参17     

孤岛油田中一区馆3单元油藏微生物多样性分析

应用分子生态学方法,分析了孤岛油田中一区馆3单元油藏样品的微生物多样性,包括两个注入水样和4口油井产出液样,发现注入水样的微生物多样性明显高于油井产出液样,其中γ-变形菌纲(Gammaproteobacteria)和β-变形菌纲(Betaproteobacteria)占较高比例;同一单元相同的油藏条件下,不同油井产出液水样中微生物多样性存在明显的差异,油井产出液中的细菌类型较单一,以Gammaproteobacteria为主,但古菌类型相对较多,包含甲烷杆菌纲(Methanobacteria)、甲烷微菌纲(Methanomicrobia)、古丸菌纲(Archaeoglobi)、热球菌纲(Thermococci)等多个不同纲的微生物.相同的油井微生物多样性随时间不同而发生变化.对油藏微生物生态结构的分析可以为微生物采油技术提供基础资料.     

Achieving Open Access to Conservation Science

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay‐per‐view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per‐article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation‐oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. Obtención de Acceso Abierto a la Ciencia de la Conservación     

Some polyphagous Homoptera gain protection from their natural enemies by feeding on the toxic plantsSpartium junceum andErythrina corallodendrum (Leguminosae)

Summary Interactions were studied among alkaloid-containing legumes (Erythrina corallodendrum andSpartium junceum) and non-toxic plants (Citrus sinensis, Cucurbita moschata andEuphorbia tirucalli), several polyphagous homopterans,Aphis craccivora (Aphididae),Icerya purchasi, I. aegyptiaca (Margarodidae),Lepidosaphes ulmi (Diaspididae) andPlanococcus citri (Pseudococcidae), and some major natural enemies of these homopterans. Significant reductions in survival due to negative effects of alkaloid containing as compared with non-alkaloidal plants were recorded for the predatorsRodolia cardinalis andChilocorus bipustulatus, but not forCryptolaemus montrouzieri (Coleoptera: Coccinellidae),Chrysoperla carnea (Neuroptera: Chrysopidae) andSympherobius sanctus (Neuroptera: Sympherobiidae). The development time of the larvae or pupae ofR. cardinalis, C. carnea andS. sanctus was longer on the toxic plants than on the non-toxic ones. The percentage of parasitism ofA. craccivora collected from the non-alkaloidal plantsVicia palaestina andMelilotus albus was much higher than that onS. junceum. The parasitoid complexes ofA. craccivora differed between both plant groups. The nutritive value of honeydew ofI. purchasi andA. craccivora, as expressed by the life span ofEncyrtus infelix (Hymenoptera: Encyrtidae) adults, was also investigated. Life spans were significantly longer when the wasps fed on honeydew produced on non-alkaloidal plants (C. sinensis andPittosporum tobira) than on alkaloid containing plants whenI. purchasi — but notA. craccivora — was the producer. It is suggested that the chemical defense ofE. corallodendrum andS. junceum is exploited by polyphagous phytophages to reduce predation. In nature, population growth and density of four of the investigated homopterans are conspicuously high when they developed on the alkaloid containing plant species, and very low on non-alkaloid plants. The efficiency of their natural enemies may be reduced by sequestration of alkaloids (or other toxic plant compounds) or their transfer into excreted honeydew. Therefore it is assumed that a generalist phytophagous homopteran may be protected from its natural enemies, although at different rates of efficiency, if it can safely sequester the host allelochemical when it develops on toxic species within its host range.     

Sequestration of cucurbitacin analogs by New and Old World chrysomelid leaf beetles in the tribe Luperini

Summary Two South American polyphagous leaf beetles,Diabrotica speciosa andCerotoma arcuata, selectively accumulated the bitter tasting compound 23,24-dihydrocucurbitacin D in their body after ingesting root tissues of cucurbit plants. Similarly, three Asian Cucurbitaceae-feeding specialists in the genusAulacophora were found to sequester the same compound. Cucurbitacin analogs were shown to deter feeding by a bird predator, indicating an allomonal role for these compounds in cucurbitacin-associated chrysomelid leaf beetles both of New and Old Worlds. The strong affinity to cucurbitacins, selective sequestration of the analogs and consequent protection from predators suggested an ecological adaptation mechanism developed in common among these two geographically isolated subtribes in the Luperini.     

Effects of Controlled Fire and Livestock Grazing on Bird Communities in East African Savannas

Abstract: In East Africa fire and grazing by wild and domestic ungulates maintain savannas, and pastoralists historically set fires and herded livestock through the use of temporary corrals called bomas. In recent decades traditional pastoral practices have declined, and this may be affecting biodiversity. We investigated the effects of prescribed fires and bomas on savanna bird communities in East Africa during the first and second dry seasons of the year (respectively before and after the rains that mark the onset of breeding for most birds). We compared abundance, richness, and community composition on 9‐ha burned plots, recently abandoned bomas, and control plots in the undisturbed matrix habitat over a 3‐year period. Generally, recently burned areas and abandoned bomas attracted greater densities of birds and had different community assemblages than the surrounding matrix. The effects of disturbances were influenced by interactions between primary productivity, represented by the normalized difference vegetation index, and time. Bird densities were highest and a greater proportion of species was observed on burned plots in the months following the fires. Drought conditions equalized bird densities across treatments within 1 year, and individuals from a greater proportion of species were more commonly observed on abandoned bomas. Yearly fluctuations in abundance were less pronounced on bomas than on burns, which indicate that although fire may benefit birds in the short term, bomas may have a more‐lasting positive effect and provide resources during droughts. Several Palearctic migrants were attracted to burned plots regardless of rainfall, which indicates continued fire suppression may threaten their already‐declining populations. Most notably, the paucity of birds observed on the controls suggests that the current structure of the matrix developed as a result of fire suppression. Traditional pastoralism appears critical to the maintenance of avian diversity in these savannas.     

What Every Conservation Biologist Should Know about Economic Theory

Abstract: The last century has seen the ascendance of a core economic model, which we will refer to as Walrasian economics. This model is driven by the psychological assumptions that humans act only in a self‐referential and narrowly rational way and that production can be described as a self‐contained circular flow between firms and households. These assumptions have critical implications for the way economics is used to inform conservation biology. Yet the Walrasian model is inconsistent with a large body of empirical evidence about actual human behavior, and it violates a number of basic physical laws. Research in behavioral science and neuroscience shows that humans are uniquely social animals and not self‐centered rational economic beings. Economic production is subject to physical laws including the laws of thermodynamics and mass balance. In addition, some contemporary economic theory, spurred by exciting new research in human behavior and a wealth of data about the negative global impact of the human economy on natural systems, is moving toward a world view that places consumption and production squarely in its behavioral and biophysical context. We argue that abandoning the straightjacket of the Walrasian core is essential to further progress in understanding the complex, coupled interactions between the human economy and the natural world. We call for a new framework for economic theory and policy that is consistent with observed human behavior, recognizes the complex and frequently irreversible interaction between human and natural systems, and directly confronts the cumulative negative effects of the human economy on the Earth's life support systems. Biophysical economics and ecological economics are two emerging economic frameworks in this movement.     

Effects of Coffee Management on Deforestation Rates and Forest Integrity

Knowledge about how forest margins are utilized can be crucial for a general understanding of changes in forest cover, forest structure, and biodiversity across landscapes. We studied forest‐agriculture transitions in southwestern Ethiopia and hypothesized that the presence of coffee (Coffea arabica)decreases deforestation rates because of coffee's importance to local economies and its widespread occurrence in forests and forest margins. Using satellite images and elevation data, we compared changes in forest cover over 37 years (1973–2010) across elevations in 2 forest‐agriculture mosaic landscapes (1100 km² around Bonga and 3000 km² in Goma‐Gera). In the field in the Bonga area, we determined coffee cover and forest structure in 40 forest margins that differed in time since deforestation. Both the absolute and relative deforestation rates were lower at coffee‐growing elevations compared with at higher elevations (?10/20% vs. ?40/50% comparing relative rates at 1800 m asl and 2300–2500 m asl, respectively). Within the coffee‐growing elevation, the proportion of sites with high coffee cover (>20%) was significantly higher in stable margins (42% of sites that had been in the same location for the entire period) than in recently changed margins (0% of sites where expansion of annual crops had changed the margin). Disturbance level and forest structure did not differ between sites with 30% or 3% coffee. However, a growing body of literature on gradients of coffee management in Ethiopia reports coffee's negative effects on abundances of forest‐specialist species. Even if the presence of coffee slows down the conversion of forest to annual‐crop agriculture, there is a risk that an intensification of coffee management will still threaten forest biodiversity, including the genetic diversity of wild coffee. Conservation policy for Ethiopian forests thus needs to develop strategies that acknowledge that forests without coffee production may have higher deforestation risks than forests with coffee production and that forests with coffee production often have lower biodiversity value. Efectos de la Administración Cafetalera sobre las Tasas de Deforestación y la Integridad de los Bosques     

Globalization of the Cashmere Market and the Decline of Large Mammals in Central Asia

As drivers of terrestrial ecosystems, humans have replaced large carnivores in most areas, and human influence not only exerts striking ecological pressures on biodiversity at local scales but also has indirect effects in distant corners of the world. We suggest that the multibillion dollar cashmere industry creates economic motivations that link western fashion preferences for cashmere to land use in Central Asia. This penchant for stylish clothing, in turn, encourages herders to increase livestock production which affects persistence of over 6 endangered large mammals in these remote, arid ecosystems. We hypothesized that global trade in cashmere has strong negative effects on native large mammals of deserts and grassland where cashmere‐producing goats are raised. We used time series data, ecological snapshots of the biomass of native and domestic ungulates, and ecologically and behaviorally based fieldwork to test our hypothesis. In Mongolia increases in domestic goat production were associated with a 3‐fold increase in local profits for herders coexisting with endangered saiga (Saiga tatarica).That increasing domestic grazing pressure carries fitness consequences was inferred on the basis of an approximately 4‐fold difference in juvenile recruitment among blue sheep (Pseudois nayaur)in trans‐Himalayan India. Across 7 study areas in Mongolia, India, and China's Tibetan Plateau, native ungulate biomass is now <5% that of domestic species. Such trends suggest ecosystem degradation and decreased capacity for the persistence of native species, including at least 8 Asian endemic species: saiga, chiru (Pantholops hodgsoni), Bactrian camel (Camelus bactrianus), snow leopard(Panthera uncia), khulan(Equus hemionus), kiang (E. kiang), takhi (E. przewalski), and wild yak (Bos mutus). Our results suggest striking yet indirect and unintended actions that link trophic‐level effects to markets induced by the trade for cashmere. Globalización del Mercado de Cachemira y la Declinación de Mamíferos Mayores en Asia Central     

The lichen-rich coastal heath vegetation on the isle of Anholt, Denmark — conservation and management

The high conservational value of the lichen-rich vegetation and landscape of the marine foreland Ørkenen on the isle of Anholt is treated from a Danish as well as a European perspective. The sensitivity of the lichen-rich vegetation to physical disturbance is emphasized. The impact of invasive species such asPinus mugo as well as the effect of atmospheric deposition of nutrients on the heaths at Anholt is described. Considerations related to the development of a management plan for Ørkenen are presented.     

Behavior and ecology of Old World Luperini beetles of the genusAulacophora (Coleoptera: Chrysomelidae)

Summary The attraction of Old World leaf beetles in the genusAulacophora to kairomones and parakairomones which are effective lures for New WorldDiabrotica andAcalymma were investigated. Beetles captured on sticky traps baited with single and multicomponent lures were no different from the control traps for two species ofAulacophora. Yellow colored traps and squash blossoms are attractive toAulacophora beetles which detect sub-microgram quantities of cucurbitacins on silica gel. Leaf feeding behavior and flight activity data are correlated with varietal preference of threeAulacophora species. The common response byDiabrotica andAulacophora to cucurbitacins reinforces the two groups' coevolutionary association with the Cucurbitaceae. The apparent lack of a common response toCucurbita blossom volatiles suggests recent evolutionary pathways are substantially different for these two groups of beetles.     

Use of stochastic patch occupancy models in the California red-legged frog for Bayesian inference regarding past events and future persistence

Assessing causes of population decline is critically important to management of threatened species. Stochastic patch occupancy models (SPOMs) are popular tools for examining spatial and temporal dynamics of populations when presence–absence data in multiple habitat patches are available. We developed a Bayesian Markov chain method that extends existing SPOMs by focusing on past environmental changes that may have altered occupancy patterns prior to the beginning of data collection. Using occupancy data from 3 creeks, we applied the method to assess 2 hypothesized causes of population decline—in situ die-off and residual impact of past source population loss—in the California red-legged frog. Despite having no data for the 20–30 years between the hypothetical event leading to population decline and the first data collected, we were able to discriminate among hypotheses, finding evidence that in situ die-off increased in 2 of the creeks. Although the creeks had comparable numbers of occupied segments, owing to different extinction–colonization dynamics, our model predicted an 8-fold difference in persistence probabilities of their populations to 2030. Adding a source population led to a greater predicted persistence probability than did decreasing the in situ die-off, emphasizing that reversing the deleterious impacts of a disturbance may not be the most efficient management strategy. We expect our method will be useful for studying dynamics and evaluating management strategies of many species.