Preservation of the genetic diversity of a local common carp in the agricultural heritage rice-fish system

Comparison of Different Deodorizing Treatments on the Flavor of Paddy Field Carp, Analyzed by the E-Nose, E-Tongue and Gas Chromatography-Ion Mobility Spectrometry

Changes in the flavor and taste profiles of Paddy Field Carp after deodorization with perilla juice (PJ), cooking wine (CW) and a mixture of the two (PJ-CW) were analyzed using the E-nose, E-tongue, gas chromatography-ion mobility spectrometry (GC-IMS), free amino acid analysis and taste nucleotide analysis. The E-nose and E-tongue revealed that deodorization reduced the content of sulfur-containing compounds, enhanced umami, bitterness, sourness and astringency, and decreased saltiness. PCA and OPLS-DA analysis successfully distinguished between the effects of the treatments. Free amino acids increased from 8777.67 to 11,125.98 mg/100 g and umami amino acids increased from 128.24 to 150.37 mg/100 g after PJ-CW deodorization (p < 0.05). Equivalent umami concentration (EUC) comparisons showed that PJ-CW treatment produced the greatest synergistic umami enhancement (to 3.15 g MSG equiv./100 g). GC-IMS detected 52 aroma compounds; PJ treatment produced the greatest diversity of aldehydes, including heptanal, nonanal, hexanal, 3-methylbutanal, (E)-2-heptenal and (E,E)-2,4-heptadienal. The total content of volatile flavor compounds was the highest after PJ-CW treatment, and the content of many characteristic flavor substances (3-hydroxy-2-butanone, benzaldehyde, 5-methyl-2(3H)-furanone) increased. These findings provided a theoretical basis for the further development of deodorization methods for Paddy Field Carp.

Cascading social-ecological benefits of biodiversity for agriculture

Cultivated species diversity can provide numerous benefits to agricultural systems. Many ecological theories have been proposed to understand the relationships between plant species diversity and trophic interactions. However, extending such theories to socioeconomic systems has been rare for agriculture. Here, we establish ten hypotheses (e.g., the natural enemy hypothesis, resource concentration hypothesis, insurance hypothesis, and aggregation hypothesis) about the relationships between cultivated species diversity (i.e., crop diversification, co-cultures of crops and domestic animals, and co-cultures of crops and edible fungi) and trophic cascades of crops, invertebrate herbivores and natural enemies in cropping systems. We then explore the socioeconomic advantages (e.g., yield, economic and environmental performance) of these trophic cascades. Finally, we propose a multi-perspective framework to promote the cascading social-ecological benefits of species diversity for agricultural sustainability. Integrating the benefits of trophic cascades into agricultural socioeconomic systems requires policies and legislation that support multi-species co-culture practices and the willingness of consumers to pay for these practices through higher prices for agricultural products.

Ethnobotanical studies on rice landraces under on-farm conservation in Xishuangbanna of Yunnan Province, China

BACKGROUND

A complex interaction and mutual influence exists among landscapes, cultures, and landraces, with rice culture being a typical embodiment of this relationship. The conservation of landraces operates alongside preserving traditional practices. The Xishuangbanna region stands out as a hub for the genetic diversity of landraces, boasting rich genetic resources. Despite the diverse rice resources in this region, a comprehensive and systematic study has not been undertaken.

METHODS

From October to November 2023, we collected rice landraces under the on-farm conservation in 18 townships including Menghai, Mengla and Jinghong in Xishuangbanna. Employing semi-structured interviews and various methods, we investigated factors influencing the preservation and loss of rice landraces in the region. Statistical analysis was applied to the agronomic traits of collected local rice, encompassing indica or japonica, glutinous or non-glutinous, grain shape, and hull color as second category traits. The second category included quantitative traits like thousand grain weight and grain length. Rice diversity among different regions, traits, and ethnic groups was assessed using the Shannon-Wiener index. Additionally, clustering analysis via the UPGMA method depicted the distribution characteristics of the resources.

RESULTS

A total of 70 rice landraces were collected in the Xishuangbanna region, each exhibiting distinct characteristics. Differences were observed across regions, trait, naming, and ethnic groups. Diversity analysis revealed that Mengla had the highest diversity, followed by Menghai, while Jinghong exhibited the lowest diversity. The second category of traits displayed broader diversity than the first, with the Dai people's glutinous rice showcasing greater diversity than other ethnic groups. Cluster analysis categorized the 70 samples into seven groups at a genetic distance of 1.15. Ethnobotanical interviews emphasized the rapid loss of rice landraces resources in Xishuangbanna, with indigenous ethnic cultures playing a vital role in the conservation of rice landraces. Dai traditions, in particular, played a crucial role in protecting glutinous rice resources, showcasing a mutual dependence between Dai culture and glutinous rice.

CONCLUSIONS

The rich natural environment and diverse ethnic cultures in Xishuangbanna have given rise to various rice landraces. The Dai, primary cultivators of glutinous rice with higher diversity, intertwine their traditional ethnic culture with the conservation of glutinous rice resources. At the same time, the preserving glutinous rice resources promotes the inheritance of Dai ethnic culture. However, rice landraces are facing the risk of loss. Hence, collecting and documenting rice landraces is crucial. Encourage local communities to sustain and expand their cultivation, promoting on-farm conservation. These measures contribute valuable germplasm and genes for rice breeding and serve as a means of cultural preservation.

Vector Biology and Integrated Management of Malaria Vectors in China

Malaria is an infectious disease caused by Plasmodium parasites, transmitted by Anopheles sinensis, Anopheles lesteri, Anopheles minimus, and Anopheles dirus in China. In 2021, the disease was eliminated in China after more than 70 years of efforts implementing an integrated mosquito management strategy. This strategy comprised indoor residual spray, insecticide-treated bed nets, irrigation management, and rice-fish coculture based on an understanding of taxonomic status and ecological behaviors of vector species, in conjunction with mass drug administration and promotion of public education. However, China still faces postelimination challenges, including the importation of approximately 2,000-4,000 cases of malaria into the country each year, as well as widespread resistance to pyrethroid insecticides in An. sinensis; these challenges require long-term vector surveillance to understand the distribution, population density, and development of resistance in vector mosquitoes to prevent local epidemics caused by imported malaria cases.

Transcriptome analysis in hepatopancreases reveals the response of domesticated common carp to a high-temperature environment in the agricultural heritage rice-fish system

Qingtian paddy field carp (PF-carp) is a local carp cultivated in the paddy field of Qingtian, Zhejiang. This rice-fish co-culture system has been recognized as one of the Globally Important Agriculture Heritage Systems (GIAHS). PF-carp has been acclimatized to the high-temperature environment of shallow paddy fields after several centuries of domestication. To reveal the physiological and molecular regulatory mechanisms of PF-carp, we chose to use 28°C as the control group and 34°C as the treatment group. We measured biochemical parameters in their serum and hepatopancreases and also performed transcriptome sequencing analysis. Compared with the control group, the serum levels of malondialdehyde (MDA), glucose (GLU), glutathione peroxidase (GSH-Px), catalase (CAT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) show no significant change. In addition, superoxide dismutase (SOD), GSH-Px, and CAT also show no significant change in hepatopancreases. We identified 1,253 differentially expressed genes (DEGs), and their pathway analysis revealed that heat stress affected AMPK signaling pathway, protein export, and other biological processes. It is worth noting that protein processing in the endoplasmic reticulum (ER) was the most significantly enriched pathway identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA). Significantly higher levels of HSP40, HSP70, HSP90, and other ubiquitin ligase-related genes were upregulated. In summary, heat stress did not lead to tissue damage, inflammation, oxidative stress, and ER stress in the hepatopancreases of PF-carp. This study provides valuable insights into the adaptation mechanism of this species to the high-temperature environment of paddy fields.

Difenoconazole disrupts carp intestinal physical barrier and causes inflammatory response via triggering oxidative stress and apoptosis

As a common fungicide, difenoconazole (DFZ) is widespread in the natural environment and poses many potential threats. Carp makes up a significant proportion of China's freshwater aquaculture population and are vulnerable to the DFZ. Therefore, this study investigated the effects of DFZ (0.488 mg/L and 1.953 mg/L) exposure for 4 d on the intestinal tissues of carp and explored the mechanisms. Specifically, DFZ exposure caused pathological damage to the intestinal tissues of carp, reducing the expression levels of intestinal tight junction proteins, and leading to damage to the intestinal barrier. In addition, DFZ exposure activated the NF-κB signaling pathway, increasing the levels of pro-inflammatory factors (TNF-α, IL-1β, IL-6) and decreasing the levels of anti-inflammatory factors (IL-10, TGF-β1). As disruption of the intestinal barrier is closely linked to oxidative stress and apoptosis, we have conducted research in both areas for this reason. The results showed that DFZ exposure elevated reactive oxygen species in carp intestines, decreased antioxidant enzyme activity, and suppressed the expression of oxidative stress-related genes. TUNEL results showed that DFZ induced the onset of apoptosis. In addition, the expression levels of apoptosis-related genes and proteins were examined. Western blotting results showed that DFZ could upregulate the protein expression levels of Bax, Cytochrome C and downregulate the protein levels of Bcl-2. qPCR results showed that DFZ could upregulate the transcript levels of Bax, Caspase-3, Caspase-8 and Caspase-9 and downregulate the transcript levels of Bcl-2 transcript levels. This suggests that DFZ can induce apoptosis of mitochondrial pathway in carp intestine. In conclusion, DFZ can induce oxidative stress and apoptosis in carp intestine, leading to the destruction of intestinal physical barrier and the occurrence of inflammation. Our data support the idea that oxidative stress and apoptosis are important triggers of pesticide-induced inflammatory bowel illness.

Mitochondrial diversity and genetic structure of common carp (Cyprinus carpio) in Pearl River and Nandujiang River

Common carp (Cyprinus carpio) is an important valuable cyprinid in China and has been a popular cultured aquaculture species around the globe. Understanding the genetic diversity of wild native common carp not only provides basic data for the protection and utilisation of common carp resources but also assesses the effect of human activities on the genetic diversity of this species. In this study, genetic diversity and population structure of the common carp from 15 sampling populations in the Pearl River and Nandujiang River were determined using a coalescent mitochondrial locus (MLS), including mitochondrial cytochrome b gene (Cytb) and a control region (D-loop) segment. The haplotype diversity and nucleotide diversity were 0.962 and 0.00628 in the Pearl River and 0.808 and 0.00376 in the Nandujiang River, respectively. Phylogenetic and haplotype network analyses indicated that three sub-species (a) C. c. rubrofuscus, (b) C. c. haematopterus and (c) C. c. carpio all occur in both rivers. AMOVA revealed that the variation within populations (86.2%) was the main source of the total variation. Statistically significant genetic differentiation among different Pearl River populations of C. c. rubrofuscus (F_st  = 0.05-0.25) and relatively high genetic differentiation between the Nandujiang River population and the Pearl River populations (F_st  > 0.238) are apparent. Bayesian clustering analyses detected that global populations consisted of eight genetic clusters and examined that Nandujiang River population included relatively pure genetic clusters. Neutrality tests suggested that native populations experienced recent population expansion, and Extended Bayesian Skyline Plot indicated that the common carp populations likely experienced a historical expansion during 0.125-0.250 MYA. Artificial fish propagation and release, escape from fish farms and Fang Sheng may explain the invasion of non-native sub-species in many river sections, such as Laibin, Rongjiang, Huizhou, Heyuan and Zhaoqing. To conserve the native common carp populations, release station should be established to culture native common carp fry. Overall, the findings can be contributed to complementing scientific knowledge for conservation and management of the wild native common carp.

Ecosystem sustainability of rice and aquatic animal co-culture systems and a synthesis of its underlying mechanisms

Integrated planting and breeding of rice and aquatic animals, including traditional rice-fish co-culture (RF), has been conducted for over 1200 years. It is one of the primary modes of modern ecologically sustainable agriculture. Rice and aquatic animal (RA) co-culture systems reduce risks of environmental pollution, reduce greenhouse gas emissions, maintain soil fertility, stabilize grain incomes, and preserve paddy field biodiversity. Nevertheless, the mechanisms that underlie the ecological sustainability of these systems remain controversial and poorly understood, restricting their practice at a larger scale. Here, the latest advance in understanding the evolution and extension of RA systems is synthesized, in addition to a discussion of the underlying ecological mechanisms of taxonomic interactions, complementary nutrient use, and microbially-driven elemental cycling. Specifically, the aim of this review is to provide a theoretical framework for the design of sustainable agricultural systems by integrating traditional knowledge and modern technologies.

Timing of Fungal Insecticide Application to Avoid Solar Ultraviolet Irradiation Enhances Field Control of Rice Planthoppers

Thechemical control of rice planthoppers (RPH)is prohibited in annual rice-shrimp rotation paddy fields. Here, the fungal insecticides Beauveria bassiana ZJU435 and Metarizhium anisoplae CQ421 were tested for control of RPH populations dominated by Nilaparvata lugens in three field trials. During four-week field trials initiated from the harsh weather of high temperatures and strong sunlight, the rice crop at the stages from tillering to flowering was effectively protected by fungal sprays applied at 14-day intervals. The sprays of either fungal insecticide after 5:00 p.m. (solar UV avoidance) suppressed the RPH population better than those before 10 a.m. The ZJU435 and CQ421 sprays for UV avoidance versus UV exposure resulted in mean control efficacies of 60% and 56% versus 41% and 45% on day 7, 77% and 78% versus 63% and 67% on day 14, 84% and 82% versus 80% and 79% on day 21, and 84% and 81% versus 79% and 75 on day 28, respectively. These results indicate that fungal insecticides can control RPH in the rice-shrimp rotation fields and offer a novel insight into the significance of solar-UV-avoiding fungal application for improved pest control during sunny summers.

Genome mining-guided activation of two silenced tandem genes in Raoultella ornithinolytica XF201 for complete biodegradation of phthalate acid esters

Phthalates (PAEs) are ubiquitous in soils and food products and thus pose a high risk to human health. Herein, genome mining revealed a great diversity of bacteria with PAEs-degrading potential. Mining of the genome of Raoultella ornithinolytica XF201, a novel strain isolated from Dongxiang wild rice rhizosphere, revealed the presence of two silenced tandem genes pcdGH (encoding protocatechuate 3,4-dioxygenase, 3,4-PCD), key aromatic ring-cleaving genes in PAEs biodegradation. Ribosome engineering was successfully utilized to activate the expression of pcdGH genes to produce 3,4-PCD in the mutant XF201-G2U5. The mutant XF201-G2U5 showed high 3,4-PCD activity and could remove 94.5 % of di-n butyl phthalate (DBP) in 72 h. The degradation kinetics obeyed the first-order kinetic model. Strain XF201-G2U5 could also degrade the other PAEs and the main intermediate metabolites, ultimately leading to tricarboxylic acid cycle. Therefore, this strategy facilitates novel bacterial resources discovery for bioremediation of PAEs and other emerging contaminants.

Thermal Stress Induces Metabolic Responses in Juvenile Qingtian Paddy Field Carp Cyprinus carpio var qingtianensis

Extreme fluctuations in water temperature lead to significant economic losses for the aquaculture industry. Cyprinus carpio var qingtianensis (locally called Qingtian paddy field carp), is a local variety commonly found in Zhejiang province, China. Unlike traditional aquaculture environments, the water temperature range between day and night in the rice field environment is much larger, and the high temperature in summer may exceed the growth threshold of fish because there is no manual intervention; therefore, the study of how the Qingtian paddy field carp (PF carp) adapts to high-temperature conditions can shed light how the species adapt to the rice field environment. To investigate the molecular mechanisms of this fish under thermal stress, the liver metabolomics of Qiangtian paddy field carp (PF carp) were analyzed. In this study, metabolomics was used to examine the metabolic reaction of PF carp (102 days old, 104.69 ± 3.08 g in weight, 14.65 ± 0.46 cm in length) at water temperatures of 28 °C (control group, CG), 34 °C (experimental group (EG) 34), and 38 °C (EG38). The results show that 175 expression profile metabolites (DEMs), including 115 upregulated and 60 downregulated metabolites, were found in the CG vs. EG34. A total of 354 DEMs were inspected in CG vs. EG38, with 85 metabolites downregulated and 269 metabolites upregulated. According to the pathway enrichment study, various pathways were altered by thermal stress, including those of lipid, amino-acid, and carbohydrate metabolism. Our study presents a potential metabolic profile for PF carp under thermal stress. It also demonstrates how the host responds to thermal stress on a metabolic and molecular level.

Genetic sources and diversity of the paddy field carp in the Pearl River basin inferred from two mitochondrial loci

Paddy field carp (PF-carp) is an economically important fish cocultured with rice in traditional agricultural systems. Several distinctive strains of PF-carp have been formed through years of artificial and cross breeding. There is a concern about the status of germplasm resources among PF-carp, since little is known about the genetic sources, diversity, or differentiation. In this study we collected 17 PF-carp populations covering Daotian carp (DTL), Ru Yuan No. 1 (RY), Jinbian carp (JBL), Shaijiang carp (SJL), and Wu carp (WL) along the Pearl River basin to explore their genetic sources and diversity using concatenated sequences of the mitochondrial cytochrome b gene and the D-Loop region. According to the haplotype network analyses, 1, 9, and 57 haplotypes originated from Cyprinus carpio carpio, Cyprinus carpio haematopterus and Cyprinus carpio rubrofuscus, respectively, confirming that genetic introgression has occurred in Pearl River PF-carp populations and Cyprinus carpio carpio was the most common species for genetic origin. The results showed that RY exhibited the lowest level of nucleotide diversity (π = 0.0011) due to high-intensity breeding and was significantly differentiated from the other four strains. PF-carp strains in these remote traditional systems tended to experience artificial selection and a lack of farmer connection that gradually increased genetic differentiation among strains. Notably, three populations of JBL exhibited significant high-level differentiation, since they originated from mountainous areas hindering farmers from fry exchange. In contrast, no significant differentiation was uncovered in the WL populations, since this strain is the most popular cultured strain and has undergone artificial exchange of parents and fry in many cultured regions. This study helps us to understand the status of germplasm resources among PF-carp and to trace their genetic origin before being introduced for local cultivation.

Effects of Protein Level on the Production and Growth Performance of Juvenile Chinese Mitten Crab (Eriocheir sinensis) and Environmental Parameters in Paddy Fields

Rice–crab co-culture systems represent integrated agriculture–aquaculture systems developed in China over the last 30 years. The rice–crab co-culture area comprised approximately 1.386 × 105 hm2 in 2019. However, there is no specific feed designed for Chinese mitten crab (Eriocheir sinensis) cultured in this system until now. In this study, we investigated feed formulae for the nutritional requirements of Chinese mitten crab in this mode. The control group was not fed with any artificial feed (Co), and the experimental groups were fed with three different feeds of 15% (T15), 30% (T30), or 45% (T45) protein content, respectively. Growth performance variations in E. sinensis were investigated along with water quality, phytoplankton, zooplankton, aquatic vascular plants, and benthic animals in the paddy fields to determine the effect of crabs and their diet on the paddy ecosystem. Dietary protein levels had no significant effect on water quality. The biomass and species of phytoplankton, zooplankton, aquatic vascular plants, and zoobenthos in the paddy field were affected by crabs and their diet. Morphological parameters of crabs were significantly more pronounced in the high-protein group than in the other groups. However, the T45 diet negatively affected production by increasing feed costs, causing precocious puberty and inducing water eutrophication. In conclusion, adding a 15% protein compound feed can meet the nutritional needs of crabs, reduce culture costs, and improve water quality. The discharged water had low ammonia nitrogen and nitrite content and no eutrophication occurred, so the water could be recycled. These findings provide a scientific reference for supporting rice and fish co-cultivation.

Metabolomic Profiling Analysis of Physiological Responses to Acute Hypoxia and Reoxygenation in Juvenile Qingtian Paddy Field Carp Cyprinus Carpio Var Qingtianensis

The Qingtian paddy field carp (Cyprinus carpio var qingtianensis) is a local carp cultivated in the rice field of Qingtian county, Zhejiang province, China. The paddy field environment is distinct from the pond environment. Due to the inability to artificially increase oxygen, the dissolved oxygen greatly changes during the day. Therefore, investigating the physiological regulation to the changes of acute dissolved oxygen in Qingtian paddy field carp (PF-carp) will dramatically clarify how it adapts to the paddy breeding environment. The high tolerance of Qingtian paddy field carp to hypoxia makes it an ideal organism for studying molecular regulatory mechanisms during hypoxia process and reoxygenation following hypoxia in fish. In this study, we compared the changes of metabolites in the hepatopancreas during hypoxia stress and the following reoxygenation through comparative metabolomics. The results showed 131 differentially expressed metabolites between the hypoxic groups and control groups. Among them, 95 were up-regulated, and 36 were down-regulated. KEGG Pathway enrichment analysis showed that these differential metabolites were mainly involved in regulating lipid, protein, and purine metabolism PF-carps could require energy during hypoxia by enhancing the gluconeogenesis pathway with core glutamic acid and glutamine metabolism. A total of 63 differentially expressed metabolites were screened by a comparison between the reoxygenated groups and the hypoxic groups. Specifically, 15 were up-regulated, and 48 were down-regulated. The KEGG Pathway enrichment analysis supported that PF-carp could continue to gain energy by consuming glutamic acid and the glutamine accumulated during hypoxia and simultaneously weaken the ammonia-transferring effect of amino acids and the toxicity of ammonia. By consuming glycerophospholipids and maintaining the Prostaglandin E content, cell damage was improved, sphingosinol synthesis was reduced, and apoptosis was inhibited. Additionally, it could enhance the salvage synthesis and de novo synthesis of purine, reduce purine accumulation, promote the synthesis of nucleotide and energy carriers, and assist in recovering physiological metabolism. Overall, results explained the physiological regulation mechanism of PF-carp adapting to the acute changes of dissolved oxygen at the metabolic level and also provided novel evidence for physiological regulation of other fish in an environment with acute changes in dissolved oxygen levels.

Genetic Diversity and Genetic Differentiation of Populations of Golden-Backed Carp (Cyprinus carpio var. Jinbei) in Traditional Rice Fields in Guizhou, China

Simple Summary

Rice-fish farming refers to the cultivation of fish in rice fields. China’s Guizhou Province has a long history (over 1000 years) of Rice-fish farming. Carp (golden-backed carp) that have been cultivated for generations in rice fields have evolved to be extremely adaptable to that environment. Unfortunately, farmers and enterprises have found that the feeding ability and growth rate of golden-backed carp are becoming increasingly weaker and slower, respectively. Therefore, the present study carried out to examine the population genetics of golden-backed, and the results indicated that the status of germplasm resources of this species is not very good. The aim of this study was to further elucidate the status of golden-backed carp germplasm resources in this province. In conclusion, this work can provide reliable fundamental data for the future conservation and breeding of golden-backed carp.

Abstract

The aim of this study was to assess the current status of the germplasm resources of golden-backed carp (Cyprinus carpio var. Jinbei) cultured in paddy fields in Guizhou Province, China. Five populations of golden-backed carp in Liping County, Jinping County, Huangping County, Congjiang County and Duyun City in Guizhou Province were subjected to high-throughput sequencing by 2b-RAD technology, and their genetic diversity and genetic differentiation were analysed. Based on sequencing, 44,896 SNP loci were obtained, and all five population genetic diversity indicators showed low diversity. In the NJ tree, the Congjiang and Liping populations were mixed together, and the other three groups formed a cluster. A cross-validation error box plot and pong cluster plot were constructed to show the K value results. When K = 1, the cross-validation error rate was the lowest. Principal component analysis showed that the Duyun population formed a group separate from the group comprising the other four populations. The genetic differentiation index and genetic distances between the Duyun population and the remaining four populations were greater than 0.05, indicating population differentiation. The genetic diversity of the five populations of golden-backed carp in Guizhou Province was low, the genetic differentiation of the Duyun population was the most significant, and the Duyun population was separate from the other four groups.

Sustainability Evaluation and Optimization on the Modern Agro-Pastoral Circular System Integrating Emergy Analysis and Life Cycle Assessment

Developing modern circular agriculture is one of the important ways to promote agricultural sustainable development, facilitating the achievement of the Sustainable Development Goals adopted by the United Nations. However, when agricultural production operators constructed particular systems, they often lacked accurate data support and parameter matching. Consequently, problems such as unknown input and output, low circulation efficiency, and lack of comprehensive evaluation occurred, increasing challenges for efficient circulation of the systems. Therefore, based on sufficient data collection and field investigation, this research integrated emergy analysis and life cycle assessment to conduct sustainability evaluation on the modern Straw–Sheep–Cropland agro-pastoral circular system. Then the system was optimized by means of coupling parameter adjustment and key technology regulation. The results showed that the whole system required lower total emergy input after optimization. And the total weighted value of potential environmental impacts of the optimized system was 47.12% of that of the original system. Meanwhile, annual environmental service emergy in air, water, and soil was reduced significantly compared with the original one. In general, the optimized system had good performance in reduction, reuse, and controllability, so its sustainability was also high. This research formed a systematic method suitable for evaluating and optimizing the modern agro-pastoral circular system, which provided accurate guidance for the scientific construction and sustainable development of circular agriculture systems.

Genetic diversity and disease: The past, present, and future of an old idea

Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.

Study Progress of Important Agricultural Heritage Systems (IAHS): A Literature Analysis

Important Agricultural Heritage Systems (IAHS), as a new type of heritage, has received extensive attention from the international scientific communities. With the increase of IAHS research, reviews on it have been conducted by many scholars. However, visualized research to show future research trends of IAHS are lacking. Therefore, using metrology analysis methods, this study aims at presenting the progress of research and the general development trends of Globally Important Agricultural Heritage Systems (GIAHS) in the world from 2006 to 2020 to provide ideas for the development of countries or regions in the future. This study mapped 292 literatures from Web of Science core collections from 2006 to 2020 by CiteSpace software. The results show that research on IAHS from 2006 to 2020 experienced two stages: the fluctuating increase stage, and the steady growth stage. Author groups from China, Italy, the USA, Japan, etc., contributed many papers on IAHS. Institutions including the Chinese Academy of Sciences, the University of Florence and the University of Padua in Italy, etc., have a relatively high influence on international IAHS research. Agriculture Ecosystems & Environment is the most cited journal. Agricultural Heritage Systems, regeneration, agriculture, agroforestry, dry-stone wall, social capital, instability, and agricultural biodiversity have been hotspots in the past 15 years. The research themes mainly focus on GIAHS, tourism, livelihood assets, and direct georeferencing. Authors in different regions concern different research themes. In the future, the fields of applications and microscopic views, social sciences, applications of standardized quantitative research methods, and broadened international cooperation should be paid more attention.

Distinct bacterial communities in the environmental water, sediment and intestine between two crayfish-plant coculture ecosystems

Microorganisms are an important part of productivity, water quality, and biogeochemical cycles in an aquaculture ecosystems and play a key role in determining the growth and fitness of aquaculture animals. Coculture ecosystems are widely applied with great significance in agricultural production worldwide. The crayfish-rice coculture ecosystem (CRCE) and crayfish-waterweed coculture ecosystem (CWCE) are two high-profile artificial ecosystems for crayfish culture. However, the bacterial communities of the environmental water, sediment, and intestine in the CRCE and CWCE remain elusive. In this study, we investigated the diversity, composition, and function of bacterial communities in water, sediment, and intestine samples from the CRCE to CWCE. The physicochemical factors of water [such as ORP (oxidation-reduction potential), TC (total carbon), TOC (total oxygen carbon), and NO₃^--N] and sediment [such as TC, TOC, TN (total nitrogen), and TP (total phosphate)] were significantly different in the CRCE and CWCE. The abundances of Proteobacteria, Actinobacteria, Verrucomicrobia, Cyanobacteria, Chlorobi, Chloroflexi, and Firmicutes were significantly different in the water bacterial communities of the CRCE and CWCE. The abundance of Vibrio in the crayfish intestine was higher in the CRCE than in the CWCE. The most abundant phyla in the CRCE and CWCE sediment were Proteobacteria and Bacteroidetes. The abundances of genes involved in transporters and ABC transporters were different in water of CRCE and CWCE. The abundances of genes involved in oxidative phosphorylation were significantly higher in the crayfish intestine of the CRCE than in that of the CWCE. Furthermore, the functional genes associated with carbon metabolism were significantly more abundant in the sediment of the CRCE than in that of the CWCE. Spearman correlation analysis and redundancy analysis (RDA) showed that the bacterial communities of the water and sediment in the CRCE and CWCE were correlated with environmental factors (pH, total carbon (TC), total oxygen carbon (TOC), total nitrogen (TN), and total phosphorus (TP)). Our findings showed that the composition, diversity and function of the bacterial communities were distinct in the environmental water, sediment, and intestine of the CRCE and CWCE crayfish coculture ecosystems due to their different ecological patterns. These results can help guide healthy farming practices and deepen the understanding of bacterial communities in crayfish-plant coculture ecosystems from the perspective of bacterial ecology. KEY POINTS: • The composition of bacterial communities in the environmental water, sediment, and intestine of the CRCE and CWCE were distinct. ̉• The abundances of genes involved in transporters and ABC transporters were different in the water of the CRCE and CWCE. • The bacterial communities of the water and sediment in the CRCE and CWCE were correlated with some environmental factors.

Soil bacterial community composition in rice-fish integrated farming systems with different planting years

The high productivity and efficient nutrient utilization in rice–fish integrated farming system are well reported. However, the characteristics of soil bacterial communities and their relationship with soil nutrient availability in rice–fish field remain unclear. In this study, we selected three paddy fields, including a rice monoculture field and two rice–fish fields with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the soil properties were significantly different among different rice farming systems. The soil bacterial community composition in the rice–fish field was significantly different from that in the rice monoculture field. Five of the top 15 phyla were observed with significant differences and Nitrospirae was the most significant one. However, no taxa observed with significance between the rice planting area and aquaculture area no matter in the 1st or 5th year of rice–fish field. RDA analysis showed that the soil bacterial community differentiation in the 5th year of rice–fish field was positively correlated with soil properties, such as AN and OM contents, EC and pH value. Although the rice yields in rice–fish field decreased, the net economic benefit of the rice–fish system enhanced obviously due to the high value of aquaculture animals.

Rice-crayfish systems are not a panacea for sustaining cleaner food production

Integrated rice-crayfish systems are expanding rapidly and are the most widely applied planting-breeding modes in Jianghan Plain in China. We conducted nutrient use efficiency, economic, and emergy analysis of three rice production modes, namely, rice monoculture (RM), rice-crayfish rotation (RCR), and rice-crayfish coculture (RCC), in Jingzhou City, which is located in the Jianghan Plain. Compared with RM mode, rice-crayfish systems using the RCR and RCC modes increased rice yield by 5-7%, showed more than 8% higher chemical nutrient use efficiency, and increased the value-to-cost ratio from 1.5-fold to 2.7-fold and the benefit-cost ratio from 2.5-fold to 3.8-fold, while decreasing irrigation water consumption and land occupation by 31% and 82-86%, respectively. RCC resulted in 10% higher crayfish yield, 12% higher phosphorus use efficiency, and 38% higher feed use efficiency than RCR. However, compared with RM, rice-crayfish systems decreased renewable fraction by 10-14%, emergy yield ratio by 9%, and emergy sustainability index by 23-26%, and they increased environmental loading ratio to 18-23%. Labor and service, fertilizer utilization, and machine and tools play important roles in these negative environmental effects. Scenario analysis showed that the rice-crayfish systems increased sustainability index by 38-45%. The technical training of new planting-breeding technology should be adopted by farmers for the efficient use of fertilizers and improvement of food yield. This study suggests that rice‑crayfish systems are not a panacea to sustain cleaner food production.

MiRNA-seq analysis of spleen and head kidney tissue from aquacultured largemouth bass (Micropterus salmoides) in response to Aeromonas hydrophila infection

Recently, the same fish diseases, which have been found in pond farming, have been found in the newly tested largemouth bass (Micropterus salmoides) system. Bacterial septicemia caused by Aeromonas hydrophila occurs frequently in largemouth bass culture leading to significant economic losses. To investigate the role miRNA in the largemouth bass disease resistance, twelve (2 tissues (spleen and head kidney) × 2 experimental groups (infected and control) × three biological replicates) small RNA libraries were constructed and sequenced with miRNA-seq. A total of 26 differentially expressed miRNAs, 8 upregulated and 18 downregulated, were identified in the spleen, and 19 differentially expressed miRNAs, 9 upregulated and 10 downregulated, were identified in head kidney (fold change ≥ 2 or ≤ 0.5 and P ≤ 0.05). The differentially expressed miRNAs with the largest fold change were selected for target gene prediction using GO and KEGG analysis. Six miRNAs in the spleen and 5 miRNAs in the head kidney were selected. Analysis showed that, of all the immune and metabolic pathways, the FoxO signaling pathway was enriched in both the spleen and head kidney groups. Common target genes of the pathway included AMP-activated catalytic subunit alpha 1 (prkaa1), phosphatidylinositol 3-kinase (pik3r3b), serine/threonine-protein kinase (plk2), and forkhead box protein G1 (foxg1a). MiRNAs (such as miR-126-5P, miR-126-3P) are involved in immune response and cell cycle functions as they regulate targeted genes in the FoxO pathway. These results will enhance our understanding of the molecular mechanisms underlying immune responses to bacterial septicemia and facilitate molecular-assisted selection of resistant strains of largemouth bass.

Genetic Diversity and Structure of Common Carp (Cyprinus carpio L.) in the Centre of Carpathian Basin: Implications for Conservation

Hungary is one of the largest common carp-production countries in Europe and now, there is a large number of local breeds and strains in the country. For proper maintenance of the animal genetic resources, information on their genetic diversity and structure is essential. At present, few data are available on the genetic purity and variability of the Hungarian common carp. In this study, we genetically analyzed 13 strains in Hungary and, in addition, the Amur wild carp, using 12 microsatellite markers. A total of 117 unique alleles were detected in 630 individuals. Low levels of genetic differentiation (Fst and Cavalli-Sforza and Edwards distance) were estimated among strains. The AMOVA showed the low but significant level of genetic differentiation among strains (3.79%). Bayesian clustering analysis using STRUCTURE classified the strains into 14 different clusters. The assignment test showed that 93.64% of the individuals could be assigned correctly into their original strain. Overall, our findings can be contributed to complementing scientific knowledge for conservation and management of threatened strains of common carp.

Rice-shrimp culture: a better intestinal microbiota, immune enzymatic activities, and muscle relish of crayfish (Procambarus clarkii) in Sichuan Province

Intestinal microbiota play an important role in the intestinal immunity and nutrient absorption, even muscle nutritional components, and the composition and function were affected by environment. In this study, the intestinal microbiota and immune enzyme, nutritional flavor of muscle of crayfish in rice field, and pond cultivation model were compared in summer and autumn. The results of Shannon diversity and Chao 1 index of intestinal microbiota based on 16S sequencing analysis showed that the diversity and abundance in autumn were higher than in summer. And the diversity and abundance of intestinal microbiota of different model in the same season were different. Four dominant phyla (relative abundance > 5% at least in one sample) of the intestinal microbiota were Bacteroidetes, Firmicutes, Proteobacteria, and Tenericutes. From summer to autumn, the intestinal immune enzyme activity of crayfish in both models showed a decreasing trend. In summer, the activity of catalase and alkaline phosphatase of crayfish cultured in the pond was significantly higher than that in rice field (P < 0.05). In autumn, the activity of catalase and lysozyme of crayfish cultured in rice field was significantly higher than that in pond (P < 0.05). The contents of umami and sweetish amino acids of muscle were higher in rice field than in pond, and the percentage of glutamic acid and alanine was significantly higher in rice field than in pond (P < 0.05). Thus, rice field model can make crayfish a more stable intestinal environment and a better intestinal immune enzyme activity and muscular flavor. Key points • The intestinal microbiota of crayfish in rice field had tended to stabilize from summer to autumn. • The crayfish had better nutrient absorption and stronger immune abilities in the rice field. • The crayfish cultured in rice field had higher overall umami concentration than in pond.

Hepatopancreas Transcriptome Profiling Analysis Reveals Physiological Responses to Acute Hypoxia and Reoxygenation in Juvenile Qingtian Paddy Field Carp Cyprinus carpio var qingtianensis

The Qingtian paddy field carp (Cyprinus carpio var qingtianensis) is a local carp cultivated in the rice field of Qingtian county, Zhejiang province, China. Its high tolerance to hypoxia makes it an ideal organism for studying the molecular regulation mechanism during hypoxia process as well as reoxygenation following hypoxia in fish. In this study, we counted the differentially expressed genes (DEGs) altered during hypoxic exposure and reoxygenation process. The results indicated that 2236 genes (1506 up-regulated genes and 730 down-regulated genes) were differentially expressed between the control and hypoxic groups. The results from Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that 1152 of 2236 genes were enriched, and those genes participated in energy metabolism, reactive oxygen species (ROS) elimination, acceleration of cell apoptosis, inhibition of growth, and other processes. We found activation of the pentose phosphate pathway in hypoxia treatment, suggesting that carbohydrates not only provide energy for metabolism but also provide NADPH for protecting the body from oxidative damage and ribosomes for promoting RNA synthesis. During reoxygenation, 4509 genes (1865 up-regulated genes and 2644 down-regulated genes) were differentially expressed. The results of KEGG enrichment analysis indicated that 2392 of 4509 genes were enriched, and participated in pyruvate and lactic acid metabolism, synthesis of amino acids and lipids, inhibition of cell apoptosis, regulation of cell growth and differentiation, and other processes. These differentially expressed genes effectively alleviate the body acidosis and promote the normal growth and development of the body. Through the analysis of KEGG pathway enrichment, we observed that the physiological regulation of Qingtian paddy field carp during the processes of hypoxia and reoxygenation is not a simple and reversible process. This work first reported the adaptive mechanism of hypoxia and the recovery mechanism of reoxygenation after hypoxia in common carp, and also provided new insights for the physiological regulation of fish under hypoxia treatment.

Genetic Diversity and Phylogeography of the Important Medical Herb, Cultivated Huang-Lian Populations, and the Wild Relatives Coptis Species in China

Huang-lian (Coptis plants in China) are essential medicinal plants in China, C. chinensis var. chinensis and C. deltoidea have been domesticated and cultivated for 700 years. In this study, the genetic diversity patterns and biogeographical information of cultivated Huang-lian and their wild relatives Coptis species were assessed using three plastids DNA regions. A total of 186 individuals from twenty-seven populations representing two species of cultivated Huang-lian and four species of wild relatives were collected and analyzed. Twenty-four haplotypes of six species were identified when three plastid spacers were combined. Historical biogeography inference revealed multiple dispersal events in the groups of cultivated Huang-lian and C. omeiensis. This evidence can infer that large initial population size and interbreeding with co-existing wild relatives in expanding new planting areas might be the main reason for maintaining the high genetic diversity of cultivated Huang-lian. Nevertheless, the multimodal curve of mismatch analysis and positive or negative differed among species and populations by neutrality tests indicated some groups of cultivated Huang-lian experienced genetic bottlenecks. Phylogeny analysis (NJ, MP, BI) showed that cultivated Huang-lian and C. omeiensis were clustered into a monophyletic group while C. chinensis var. brevisepala was paraphyletic, having earlier divergence time from C. chinensis var. chinensis (7.6 Ma) than C. omeiensis. Parsimony network demonstrated that C. deltoidea had more shared haplotypes with C. omeiensis than C. chinensis var. chinensis, and other haplotypes of C. deltoidea and C. omeiensis had less mutation steps than that of C. chinensis var. chinensis and C. omeiensis. This evidence suggests that C. omeiensis has a closer relationship with cultivated Huang-lian and might be a potential wild relative to C. deltoidea. The results reported here provide the baseline data for preserving genetic resources of Huang-lian and also evaluating the genetic impacts of long-term cultivation on medicinal plants, which could be instructive to future cultivation projects of traditional Chinese medicinal plants.

Research Progress in the Conservation and Development of China-Nationally Important Agricultural Heritage Systems (China-NIAHS)

To cope with the problem of the global agricultural environment, food security, and the crisis of sustainable agricultural development, the Food and Agriculture Organization (FAO), together with other relevant national organizations and several countries, launched the Globally Important Agricultural Heritage Systems (GIAHS) in 2002. The Qingtian Rice-Fish system was designated as China’s first GIAHS and was included in the first batch of GIAHS pilot sites, in 2005. Since then, study of systematic agricultural heritage and its conservation and development has progressed in China. On the basis of a comprehensive collection of relevant studies, the author reviews the main achievements in conservation and development of China-Nationally Important Agricultural Heritage Systems (China-NIAHS) over the past 15 years. At the present stage, the core contents of study on agricultural heritage are focused on two aspects. One is the benefit of exploration with multi-functional development. Another is dynamic conservation with adaptive management. There are many controversies around the concept and connotation of agricultural heritage, which, in turn, promote the understanding of this new type of heritage. The sustainable mechanism within agricultural heritage gives itself value diversity. Study about the value of agricultural heritage highlights the significance of conservation. The development of multi-functional industrials based on its multi-functional value is the pathway for the development of China-NIAHS, including the production of high-quality and characteristic local agricultural products, the development of ecotourism, and the development of cultural industries. To carry out dynamic conservation and adaptive management, the establishment of "five in one" benefit-sharing, multi-stakeholder mechanisms, legally guaranteed incentive mechanisms, government-leading, multi-financing mechanisms, and multi-disciplinary scientific support mechanisms are indispensable. Although China has made great progress in the study of agricultural heritage, it still needs to carry out additional research through heritage resources surveys, regular patterns of system evolution, and sustainable mechanisms, as well as perform more applicable research in framework and mechanism construction and paradigms of dynamic protection. Multidisciplinary comprehensive studies are necessary as well.

The maintenance of stable yield and high genetic diversity in the agricultural heritage torreya tree system

BACKGROUND

Understanding how traditional agriculture systems have been maintained would help design sustainable agriculture. In this study, we examined how farmers have used two types of local trees (Torreya grandis) for stable yield and maintaining genetic diversity in the "globally important agricultural heritage torreya tree system". The two type of torreya trees are grafted torreya (GT) tree and non-grafted-torreya (NGT) tree. The GT tree has only female and was used to produced seed yields. The NGT tree has both male and female and was used to support GT tree by providing pollens and rootstocks. We first tested the ratio of GT tree to NGT tree, their age groups, ratio of female trees (including GT and NGT trees) to male, and the flowering period of GT and NGT trees. We then tested seed yields and genetic diversity of GT and NGT trees. We further tested gene flow among NGT trees, and the relationship of gene flow with exchange rates of pollens and seeds.

RESULTS

GT and NGT trees (male and female) were planted in a mosaic pattern with a ratio of 4:1 (GT:NGT). In this planting pattern, one NGT male trees provided pollen for 20 female trees of GT and NGT. The trees were classified into four age groups (I = 100-400 years old; II = 400-700 years old; III = 700-1000 years old; and IV = 1000-1300 years old) based on basal diameter. The entire flowering period was longer for NGT trees than for GT trees that ensured GT trees (which lack of males) being exposed to pollens. GT tree had high and stable seed yield that increased with age groups. High genetic diversity has been maintained in both rootstocks of the GT trees and NGT trees. There was a strong gene flow among NGT trees, which positive correlated with the exchange rates of pollens and seeds.

CONCLUSIONS

Our results suggest that farmers obtain stable seed yields, and maintain high genetic diversity by ingeniously using the local GT tree as yield producer and NGT tree as supporter. These GT and NGT trees together ensure sustainable torreya production.

Microbial Community Structures and Important Associations Between Soil Nutrients and the Responses of Specific Taxa to Rice-Frog Cultivation

Rice-frog cultivation is a traditional farming system in China and has been reintroduced as an agricultural practice in China in recent years. The microbial community in paddy rhizospheric soils has attracted much attention because many microorganisms participate in functional processes in soils. In this study, Illumina MiSeq sequencing-based techniques were used to investigate soil microbial communities and functional gene patterns across samples obtained by conventional rice cultivation (CR) and rice-frog cultivation (RF). The results showed that RF significantly affected the microbial community composition and richness, which indicated that the rhizospheric microorganisms responded to the introduction of tiger frogs into the paddy fields. Operational taxonomic units (OTUs) from Sandaracinaceae, Anaerolineaceae, Candidatus Nitrososphaera, Candidatus Nitrosotalea, Candidatus Nitrosoarchaeum and some unclassified OTUs from Euryarchaeota and Agaricomycetes were significantly enriched by RF. The abiotic parameters soil organic carbon (SOC), nitrate nitrogen (NO3 --N), and available phosphorus (AP) changed under RF treatment and played essential roles in establishing the soil bacterial, archaeal, and fungal compositions. Correlations between environmental factors and microbial communities were described using network analysis. SOC was strongly correlated with Anaerolineaceae, Methanosaeta, and Scutellinia. NO3 --N showed strong positive correlations with Opitutus, Geobacter, and Methanosaeta. NH4 ++-N was strongly positively associated with Sideroxydans, and TN was strongly positively correlated with Candidatus Nitrotoga. Compared to conventional CR, RF greatly enriched specific microbial taxa. These taxa may be involved in the decomposition of complex organic matter and the transformation of soil nutrients, thus promoting plant growth by improving nutrient cycling. The unique patterns of microbial taxonomic and functional composition in soil profiles suggested functional redundancy in these paddy soils. RF could significantly affect the bacterial, archaeal, and fungal communities though changing SOC and AP levels.

Microplastic pollution in rice-fish co-culture system: A report of three farmland stations in Shanghai, China

Microplastics are emerging contaminants of increasing concern. Despite the occurrence of microplastics in farmland soils, the knowledge on microplastics in rice-fish co-culture ecosystems is limited. In this study, we investigated the distribution of microplastics in three rice-fish culture stations in Shanghai. During non-rice and rice-planting periods, microplastics in water, soils and aquatic animals (eel, loach and crayfish) were systematically assayed using methods of NaCl density extraction, H₂O₂ digestion and micro-fourier transform infrared spectroscopy. Results showed that average microplastic abundances were 0.4 ± 0.1 items L^-1, 10.3 ± 2.2 items kg^-1, 1.7 ± 0.5 items individual^-1 in water, soils and aquatic animal samples, respectively. We found an increasing trend in microplastic abundances in water, soil and animal samples from non-rice period to rice-planting period. Almost all of microplastics were found in digestive tracts of animals. Major microplastics were small (<1 mm) polyethylene and polypropylene fibers, with color of white and translucent. Size, shape, color and polymer type distributions of microplastics were similarly found in environmental and animal samples. Moreover, microplastic abundances in aquatic animals correlated to abundance in farmland soils. This study, for the first time, reveals the occurrence and characteristics of microplastic pollution in rice-fish culture ecosystem which suggests the potential ecological risks of microplastics in the agroecosystem.

Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns

Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.