Cryptic occurrence of <Emphasis Type="Italic">Chattonella marina</Emphasis> var. <Emphasis Type="Italic">marina</Emphasis> in mangrove sediments in Probolinggo,East Java Province,Indonesia

Mangrove forests and adjacent creeks are known to be highly productive estuaries, which are partly supported by benthic microalgae that grow on the sediments. During surveys investigating the microalgal floras of mangrove swamps in the eastern part of Java Island, a mud sample unexpectedly included large numbers of a notorious fish killer, Chattonella-like motile cells, and its resting cysts. These motile cells were established as clonal cultures for further identification and physiological tests. The cysts were examined through palynological and molecular biological means. Identification based on light microscopy and ribosomal RNA gene sequences confirmed that these cells and cysts were Chattonella marina var. marina. While the strains were genetically identical to the temperate strains isolated from Japan and China, temperature experiments showed that the Indonesian strains possessed a high maximum quantum yield of photosystem II even after exposure to 34 °C, a temperature at which the Japanese strain could not survive. Salinity experiments showed adaptation of the strains to a salinity of 15. These findings, together with the discovery of populations of cysts in the mangrove sediment, highlight the tough and unique nature of the Indonesian strains, which are likely adapted to wide fluctuations of temperature and salinity in mangrove swamps, and pose a potential risk to fisheries in Indonesia.     

Optimisation of larval culture of the mussel <Emphasis Type="Italic">Mytilus</Emphasis><Emphasis Type="Italic">edulis</Emphasis> (L.)

The blue mussel Mytilus edulis is a commercially important species whose fishery and culture generally relies on natural spat collection. Hatchery-production could provide an alternative source of seed, enabling reliable expansion of the industry. Mussel spawning and larval rearing trials were carried out to optimise elements of hatchery production. Culturing fertilised eggs at low density (20–200 eggs cm⁻²) rather than high density (400–720 eggs cm⁻²) significantly improved the quality of first veliger larvae and differences in this improvement were evident between the eggs from different females (maternal effects). Veliger larval growth at 17 or 21°C was significantly faster than growth at 14°C. Feeding veliger larvae an identical total ration either daily or at 2–3 day intervals did not significantly affect their growth. Different microalgal diets (1: Isochrysis sp. (clone T-ISO), 2: Chaetoceros calcitrans forma pumilus, 3: C. muelleri, 4: mixed Isochrysis sp. (clone T-ISO) and C. calcitrans f. pumilus, and 5: mixed Isochrysis sp. (clone T-ISO) and C. muelleri) were tested on veliger larval growth and mixed diets outperformed single-species diets.     

Analysis of rice blast resistance gene <Emphasis Type="Italic">Pi</Emphasis>-<Emphasis Type="Italic">z</Emphasis> in rice germplasm using pathogenicity assays and DNA markers

The Pi-z gene in rice confers resistance to a wide range of races of the rice blast fungus, Magnaporthe oryzae. The objective of this study was to characterize Pi-z in 111 rice germplasm accessions using DNA markers and pathogenicity assays. The existence of Pi-z in rice germplasm was detected by using four simple sequence repeat (SSR) markers (RM527, AP4791, AP5659-1, AP5659-5) closely linked to Pi-z, and was verified using pathogenicity assays with an avirulent strain (IE1k) and two virulent races (IB33 and IB49). Among 111 germplasm accessions evaluated, 73 were found to contain the Pi-z gene using both SSR markers and pathogenicity assays. The remaining 38 germplasm accessions were found to be inconsistent in their responses to the blast races IB33, IEIk and IB49 with expected SSR marker alleles, suggesting the presence of unexpected SSR alleles and additional R gene(s). These characterized germplasm can be used for genetic studies and marker-assisted breeding for improving blast resistance in rice.     

Functional and structural responses of bacterial and fungal communities from paddy fields following long-term rice cultivation

Purpose

Rice paddy soils undergo pedogenesis driven by periodic flooding and drainage cycles that lead to accumulation of organic matter and the stratification of nutrients and oxygen in the soil profile. Here, we examined the effects of continuous rice cultivation on microbial community structures, enzyme activities, and chemical properties for paddy soils along a chronosequence representing 0–700 years of rice cropping in China.

Materials and methods

Changes in the abundance and composition of bacterial and fungal communities were characterized at three depths (0–5, 5–10, and 10–20 cm) in relation to organic carbon, total nitrogen, dissolved organic carbon, microbial biomass carbon/nitrogen, and activities of acid phosphatase, invertase, and urease.

Results and discussion

Both soil organic carbon and total nitrogen increased over time at all three depths, while pH generally decreased. Microbial abundance (bacteria and fungi) and invertase and urease activity significantly increased with the duration of rice cultivation, especially in the surface layer. Fungal abundance and acid phosphatase activity declined with depth, whereas bacterial abundance was highest at the 5–10-cm soil depth. Profiles of the microbial community based on PCR-DGGE of 16S rRNA indicated that the composition of fungal communities was strongly influenced by soil depth, whereas soil bacterial community structures were similar throughout the profile.

Conclusions

Soil bioactivity (microbial abundance and soil enzymes) gradually increased with organic carbon and total nitrogen accumulation under prolonged rice cultivation. Microbial activity decreased with depth, and soil microbial communities were stratified with soil depth. The fungal community was more sensitive than the bacterial community to cultivation age and soil depth. However, the mechanism of fungal community succession with rice cultivation needs further research.

     

Assessing the Impacts of Time-to-Detection Distribution Assumptions on Detection Probability Estimation

Abundance estimates from animal point-count surveys require accurate estimates of detection probabilities. The standard model for estimating detection from removal-sampled point-count surveys assumes that organisms at a survey site are detected at a constant rate; however, this assumption can often lead to biased estimates. We consider a class of N-mixture models that allows for detection heterogeneity over time through a flexibly defined time-to-detection distribution (TTDD) and allows for fixed and random effects for both abundance and detection. Our model is thus a combination of survival time-to-event analysis with unknown-N, unknown-p abundance estimation. We specifically explore two-parameter families of TTDDs, e.g., gamma, that can additionally include a mixture component to model increased probability of detection in the initial observation period. Based on simulation analyses, we find that modeling a TTDD by using a two-parameter family is necessary when data have a chance of arising from a distribution of this nature. In addition, models with a mixture component can outperform non-mixture models even when the truth is non-mixture. Finally, we analyze an Ovenbird data set from the Chippewa National Forest using mixed effect models for both abundance and detection. We demonstrate that the effects of explanatory variables on abundance and detection are consistent across mixture TTDDs but that flexible TTDDs result in lower estimated probabilities of detection and therefore higher estimates of abundance.Supplementary materials accompanying this paper appear on-line.     

农业机械化发展水平的概率-灰色评估方法及应用

在建立农业机械化发展水平评估指标体系的基础上，结合不确定性理论及灰色系统理论，提出了评估农业机械化发展水平的新方法——概率－灰色评估法。并用该方法对河南省农业机械化发展水平进行了评估分析。     

小麦秆锈菌生理小种鉴别寄主及命名方法的演变

为了监测小麦秆锈菌生理小种变化动态及其毒力变异规律,为预防Ug99入侵并开展相应抗源筛选创新提供参考,全面介绍了国内外不同时期小麦秆锈菌生理小种的鉴别寄主及相应的小种命名法的演变情况：(1)Stakman′s标准鉴别寄主与小种命名;(2)Roelfs单基因鉴定法的鉴别寄主与小种命名;(3)中国当前和以后拟采用的小麦秆锈菌小种鉴定的鉴别寄主名称与小种命名。这些介绍将有助于小麦秆锈病研究者与育种学家间的信息交流。     

Plant diversity of secondary forests in response to anthropogenic disturbance levels in montane regions of northeastern China

The effects of anthropogenic disturbances on forest structure and plant diversity of secondary forest ecosystems were evaluated based on the classification by site factors in the montane regions of northeastern China. Forty-five sample plots containing 720 sub-plots of overstory species (8 m × 8 m), 1,440 quadrats of understory species (2 m × 2 m), and 1,440 quadrats of herbaceous layer species (1 m × 1 m) were clustered into five groups (G1, G2, G3, G4 and G5) by site variables with Hierarchical Cluster Analysis. Meanwhile, the disturbance levels corresponding to the five groups were determined according to the factors influencing human disturbances (D0-G2, D1-G1, D2-G3, D3-G5, and D4-G4). Species diversities of overstory, understory, herbaceous layer and overall species were evaluated using species number, Margalef index, Pielou index, Shannon–Wiener index, and Simpson index; and β-diversities (Whittaker index, Cody index). Basal area of stands exhibited a decreasing trend along the disturbance level due to a gradual increase in the extraction of timber by the human disturbances. The indices of species diversity suggested that overstory and understory species were distributed evenly among the groups or disturbance levels. There were no absolutely dominant tree species in the secondary forest ecosystems. The differences in site factors and the current disturbance intensities were not intense enough to lead to loose changes in overstory and understory species. The species diversity indices exhibited the maximum values at D3 (G5) for herbaceous layer species; this may suggest that the current disturbance intensities were intense enough to lead the changes of herbaceous layer species. Three rare and endangered species (Juglans mandshurica, Fraxinus mandshurica and Acanthopanax senticosus) were found within the secondary forests. These rare and endangered species appeared in each clustered group or disturbance level, which suggested that the current disturbance intensity in the study area was not strong enough to influence the distribution of rare and endangered species. The current disturbances in the secondary forests may not lead to a decrease in stability and complexity of the overstory and understory species, but the higher disturbance level may be intense enough to change the habitat fitness for the herbaceous species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized authors.     

孕穗期低温条件下ABA对水稻结实率及叶片生理特性的影响

为了明确ABA对孕穗期低温下水稻结实率及叶片生理特性的调控效应,本试验在盆栽条件下,以2个水稻(Oryza sativa L.)品种‘龙粳11’（冷敏型）和‘龙稻5’（耐冷型）为材料,于孕穗期在人工气候室进行低温（15℃,持续1,2,3,4,5天）处理,并喷施不同浓度的脱落酸(ABA),研究低温条件下ABA对不同水稻结实率的调控效应,同时探讨了ABA和低温对水稻叶片膜透性、抗氧化酶等生理特性的影响。结果表明：低温条件下,‘龙稻5’的结实率变化不大,‘龙粳11’的结实率显著降低,20 mg/L的ABA能够有效缓解低温伤害,相对提高低温胁迫下水稻的结实率。叶片超氧化物歧化酶(SOD)、过氧化物酶(POD)和过氧化氢酶(CAT)活性表现出先升高后下降的变化趋势,‘龙稻5’的抗氧化酶活性、可溶性糖和可溶性蛋白含量高于‘龙粳11’,但丙二醛(MDA)含量和相对电导率低于‘龙粳11’。ABA可提高冷敏品种的抗氧化酶活性、可溶性糖和可溶性蛋白的含量,同时可降低MDA含量和相对电导率。这说明ABA可以通过调控水稻抗氧化酶、可溶性糖等生理指标的活性及含量,进而提高冷敏水稻品种的耐冷性。     

Aflatoxin B<Subscript>1</Subscript> (AFB<Subscript>1</Subscript>) reduces growth performance,physiological response,and disease resistance in Tra catfish (<Emphasis Type="Italic">Pangasius hypophthalmus</Emphasis>)

Triplicate groups of one hundred Tra catfish (8 g?±?0.2) were fed seven test diets containing increasing levels of AFB₁ (0, 50, 100, 250, 500, and 1000 μg AFB₁ kg^?1). Additionally Mycofix® Secure was added at 1.5% to one diet containing 500 μg AFB₁ kg^?1. Results showed that Tra catfish are sensitive to AFB₁. Reduction in weight gain (P?<?0.05) was observed for fish fed 50 μg AFB₁ kg^?1 and declined further with increasing levels of AFB₁ in the diets. Fish fed diets contaminated with 500 and 1000 μg AFB₁ kg^?1 showed increased (P?>?0.05) hepatosomatic index (HIS), while an increase in adipose somatic index (ASI) was observed in fish fed 50 μg AFB₁ kg^?1 and above when compared to the control and Mycofix® diets. After 12 weeks, blood serum analysis revealed higher alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels in fish fed the 50, 100, and 250 μg AFB₁ kg^?1 suggesting occurrence of liver damage. Disease resistance of fish exposed to Edwardsiella ictaluri was also compromised by the presence of AFB₁ in the feed and was directly related to the contamination level. Seven days after Edwardsiella ictaluri exposure, survival rates were 50, 41.7, 31.7, and 8.3% for fish fed control, 50, 100, and 250 μg AFB₁ kg^?1, respectively. This trial shows that AFB₁ at a level of 50 μg AFB₁ kg^?1 and above can affect fish performance and disease resistance. Application of an effective mycotoxin management in the feed seems to be useful to prevent the negative effects of AFB₁.