A long-ignored unique ecosystem of cavefishes in the southern karst: achievements, challenges, and prospects.

Cavefishes represent a taxon that has experienced natural selection pressures. This paper summarizes the results with respect to the taxonomy, diversity, phylogeny, and adaptation aspects of cavefishes research. It showed that: 1) These studies suggest that cavefishes play important roles in the study of geologic history and adaptation to extreme environments, but the mechanisms involved 168 species of cavefishes belonging to 17 genera, four families, and two orders have been recorded in China. Meanwhile, more new species are being discovered recently, and the species diversity of cavefishes are still underestimated, indicating the need to strengthen the survey in field. 2) The biogeography of cavefishes have focused on Sinocyclocheilus and Triplophysa, that have helped understand the geomorphology of karst areas in southern China and the spatial pattern of species diversity. These studies revealed the influences of evolution and geological history in Sinocyclocheilus, but there are still many species that have not been studied accordingly. 3) Some adaptive mechanistic studies have been conducted on cavefishes, primarily focusing on eye and body color degradation and energy metabolism in the genus Sinocyclocheilus to reveal adaptive mechanisms in the dark environment. 4) The IUCN list of protected cavefishes species in China only includes 21 species. The List of Key Protected Wild Animals for 2021 includes all species of Sinocyclocheilus as National Class II.It is necessary to strengthen the research on the biodiversity and adaptation and need consider the conservation actions for cavefishes.

Microbial Species-Area Relationships on the Skins of Amphibian Hosts.

Unlike species-area relationships (SARs) that have been widely reported for plants and animals on Earth, there is no clear understanding of the SARs for microorganisms. In this study, 358 specimens of 10 amphibian host species collected from the rural Chengdu region of southwest China were selected as island models for evaluating SAR curve shapes and assessing the skin microbiota from different amphibian species. The results showed that skin microbial diversity, measured using Hill's number, presented significant differences between hosts, but the difference was insignificant between habitat-specific classifications of hosts. As for microbial SARs, other than the classical power-law (PL) model describing an expected steady increase in microbial diversity as sampled skin area increases, two additional trends were observed: (i) microbial diversity first rises and gradually decreases after reaching a maximum accrual diversity (MaxAD) and (ii) microbial diversity decreases and starts to rise after reaching the minimum accrual diversity (MinAD). Among the four SAR statistical models compared, it was consistently found that the models that can describe MaxAD were favorably selected in the highest frequency. Models that can describe MinAD and PL model also performed reasonably well. However, PL had the poorest fitting power, implying the necessity of introducing biologically meaningful complex SAR models in microbial diversity research. In conclusion, through multihost analyses, our study provided compelling evidence that microbial SARs are complex and nonlinear. A variety of ecological mechanisms may be used for explaining these, including, but not limited to, community saturation, small-island effects, or sampling heterogeneity. IMPORTANCE In this study, we investigate species-area relationships (SARs) for skin-borne symbiotic microbes of wildlife hosts. Unlike the traditional SARs for plants and animals, symbiotic microbial SARs were complex. We found that both U-shaped and inverted U-shaped SAR models were widely favored for microbial taxa than the well-known power-law model in different host species. These favored models presented interesting statistical features, including minimal or maximal accrual diversity or inflection point. We provide intuitive derivations of these statistical properties. We showed that different habitat-specific amphibian hosts did not present distinct microbial diversity and skin-related SAR patterns. We predicted that approximately 600 to 1,400 cm2 (in two-dimensional [2D] measurement) or approximately 1,200 to 3 500 cm2 (in 3D measurement) are the skin area threshold range that can allow the emergence of minimal or maximal accrual microbial diversity with high chances. Finally, we list a variety of ecological mechanisms that may be used for explaining the observed nonlinear SAR trends.

Diversity and distribution of culturable fouling bacteria in typical mariculture zones in Daya Bay, South China.

The diversity and distribution of culturable fouling bacteria in shellfish, fish and non-mariculture zones in Daya Bay were investigated by using a traditional culture-dependent approach combined with an analysis of bacterial 16S rRNA gene sequences. A total of 129 isolates of fouling bacteria belonging to 37 species in 25 genera were collected and identified, which indicated that the three different mariculture zones harbored abundant and diverse fouling bacterial community. At the genus level, Pseudomonas, Arcobacter and Curtobacterium dominated the fouling bacterial community. Moreover, approximately 46% of the 37 representative isolates could form biofilms. After comparing the diversity and distribution of the biofilm-forming bacteria in three different mariculture zones, it was concluded that the ratios of biofilm-forming bacteria in shellfish (68.4%) and fish (63.4%) in mariculture zones were much greater than those in non-mariculture (42.0%) zone. These results provide important information, for the first time, regarding the fouling bacterial community in typical mariculture zones in South China, which will establish a foundation to develop strategies for biofilm control and disease defense.

Genomic insights into the diversity of non-coding RNAs in Bacillus cereus sensu lato.

Bacillus cereus sensu lato is a group of bacteria of medical and agricultural importance in different ecological niches and with controversial taxonomic relationships. Studying the composition of non-coding RNAs (ncRNAs) in several bacterial groups has been an important tool for identifying genetic information and better understanding genetic regulation towards environment adaptation. However, to date, no comparative genomics study of ncRNA has been performed in this group. Thus, this study aimed to identify and characterize the set of ncRNAs from 132 strains of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis to obtain an overview of the diversity and distribution of these genetic elements in these species. We observed that the number of ncRNAs differs in the chromosomes of the three species, but not in the plasmids, when species or phylogenetic clusters were compared. The prevailing functional/structural category was Cis-reg and the most frequent class was Riboswitch. However, in plasmids, the class Group II intron was the most frequent. Also, nine ncRNAs were selected for validation in the strain B. thuringiensis 407 by RT-PCR, which allowed to identify the expression of the ncRNAs. The wide distribution and diversity of ncRNAs in the B. cereus group, and more intensely in B. thuringiensis, may help improve the abilities of these species to adapt to various environmental changes. Further studies should address the expression of these genetic elements in different conditions.

Three new goatfishes of the genus Upeneus from the Eastern Indian Ocean and Western Pacific, with an updated taxonomic account for U. itoui (Mullidae: japonicus-species group).

Coastal marine fish diversity from E India and Indonesia to S Japan is still insufficiently investigated. Of the 42 species of goatfishes (Mullidae) recorded from this area, 12 were described only since 2010 and ten of those belong to the genus Upeneus. During a recent review of species of Upeneus of the so-called japonicus-species group (characterized by seven dorsal-fin spines), 13 specimens that had been previously identified as U. guttatus from Indonesia and Vietnam were found to be distinct, representing possibly two undescribed species. These specimens were studied together with 20 U. itoui from S Japan, a rather similar species, and a yet unidentified congeneric from S Japan. In total 41 morphometric, 10 meristic and several colour characters were examined and detailed comparisons with a large data set from all 14 japonicus-group species conducted. Three new species, U. dimipavlov n. sp. from Nha Trang, S-central Vietnam, U. elongatus n. sp. from Tanega-shima Island, Kagoshima, S Japan and U. willwhite n. sp. from Lombok, S Indonesia are described and an updated account for U. itoui is provided. Among these four featured species, U. elongatus is the most different, having more gill rakers, the shallowest head and body and distinct colour patterns on caudal and dorsal fins. Upeneus dimipavlov differs from the remaining two species in having a more rounded and less laterally compressed body with a wider caudal peduncle and no conspicuous mid-lateral body stripe in fresh fish. Upeneus willwhite differs from U. itoui in deeper head, larger eyes, longer upper jaw and barbels and oblique bars on the lower caudal-fin lobe which do not cross the entire lobe. Additional comparisons of each of the four featured species with all other japonicus-group species and U. heterospinus were conducted providing evidence for distinction and differential diagnosis. Unvouchered in-situ photographs of four goatfish specimens from the Central Philippines that resemble U. elongatus in caudal- and dorsal-fin colour patterns are presented. The need for further sampling and associated taxonomic investigations as prerequisites for appropriate assessment of ecological and conservation parameters such as diversity, distribution and rarity is emphasized in the discussion.

Diversity, abundance, and distribution of anammox bacteria in shipping channel sediment of Hong Kong by analysis of DNA and RNA.

Anammox bacteria have been detected in various ecosystems, but their occurrence and community composition along the shipping channels have not been reported. In this study, anammox bacteria were recovered by PCR-amplified biomarker hzsB gene from the genomic DNA of the sediment samples. Phylogenetic tree revealed that Candidatus Scalindua and Ca. Brocadia dominated the anammox community of the Hong Kong channels; Ca. Scalindua spp. was present abundantly at the sites farther from the shore, whereas Ca. Jettenia and Ca. Kuenenia were detected as the minor members in the estuarine sediments near the shipping terminals. The highest values of Shannon-Wiener index and Chao1 were identified in the sediments along the Urmston road (UR), suggesting the highest α-diversity and species richness of anammox bacteria. PCoA analysis indicated that anammox bacterial communities along UR and Tai Hong (TH) channel were site-specific because these samples were grouped and clearly separated from the other samples. The maximum diversity of anammox bacteria was detected in UR samples, ranging from 6.28 × 105 to 1.28 × 106 gene copies per gram of dry sediment. A similar pattern of their transcriptional activities was also observed among these channels. Pearson's moment correlation and redundancy analysis indicated that NH4+-N was a strong factor shaping the community structure, which showed significant positive correlation with the anammox bacterial abundance and anammox transcriptional activities (p < 0.01, r > 0.8). Also, NH4+-N, (NO3- + NO2-)-N, and NH4+/NOX were additional key environmental factors that influenced the anammox community diversity and distribution. This study yields a better understanding of the ecological distribution of anammox bacteria and the dominant genera in selective niche.

Termite Diversity in Urban Landscape, South Jakarta, Indonesia.

The population of South Jakarta, a city within the Province of Jakarta Capital Region, is increasing annually, and the development of land into building causes termite diversity loss. The aim of this research was to determine the diversity of subterranean termite species and their distribution in South Jakarta and to evaluate the soil profile termite habitat. This study was conducted in South Jakarta and was carried out at four residential areas representing four randomly selected sub-districts. Specimens were collected with a baiting system. At each residence, as many as 25-30 stakes of pine wood (Pinus merkusii) sized 2 cm × 2 cm × 46 cm were placed for termite sampling. Soil samples were also collected from each residence for testing of their texture, pH, soil water content, and C-organic. Three species of subterranean termites were identified, including Coptotermes curvignathus, Microtermes insperatus, and Macrotermes gilvus, with area-specific variations in occurrence. The soil and weather conditions in the studied areas provided suitable habitat for termites, and M. insperatus was the most commonly found species.

Diversity and effect of Trichoderma spp. associated with green mold disease on Lentinula edodes in China.

Lentinula edodes, one of the most important edible mushrooms in China, is affected heavily by the infection of green mold that overgrows mushroom mycelia. We collected the diseased samples from main L. edodes cultivation regions in China to characterize the pathogen and to study the effect of Trichoderma spp. on L. edodes species. We identified six Trichoderma species, that is, T. harzianum, T. atroviride, T. viride, T. pleuroticola, T. longibrachiatum, and T. oblongisporum based on the internal transcribed spacer or tef1-α sequences and morphology characteristics. In confrontation cultures on Petri plates or in tubes, and in L. edodes cultures in a medium containing Trichoderma metabolites, L. edodes mycelia were not only distorted and swollen, but also inhibited by Trichoderma isolates. It is not possible that adjusting pH value or temperature is used for controlling L. edodes green disease, because the growth of most of Trichoderma isolates and L. edodes shared similar pH and temperature conditions.

Diversity and distribution of host animal species of hantavirus and risk to human health in Jiuhua mountain area, China.

OBJECTIVE: To investigate the diversity and the distribution of host animal species of hantavirus and the effect on human health in Jiuhua Mountain area, China. METHODS: The host animal species of hantavirus was surveyed by using the trap method and the species diversity was evaluated by using the Simpson, Shannon-Weaner, and Pielou indices. Hantavirus antigens or antibodies in lung and blood samples of all the captured host animals were detected by direct or indirect immunofluorescence. RESULTS: Nine animal species of hantavirus were distributed in the forest ecosystem of Jiuhua Mountain. Of these, Niviventer confucianus and Apodemus agrarius were predominant, and N. confucianus, Rattus norvegicus, and Mus musculus had relatively large niche breadth index values. The host animals in the eastern and western mountain regions shared similar biodiversity index characteristics, predominant species, and species structures. Hantavirus was detected in 5 host animal species in Jiuhua Mountain area, the carriage rate of hantavirus was 6.03%. The average density of host animals in forest areas of the mountainous area was only 2.20%, and the virus infection rate in the healthy population was 2.33%. CONCLUSION: The circulation of hantavirus was low in the forest areas of Jiuhua Mountain and did not pose a threat to human health.

Diversity and distribution of host animal species of hantavirus and risk to human health in Jiuhua mountain area, China / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To investigate the diversity and the distribution of host animal species of hantavirus and the effect on human health in Jiuhua Mountain area, China.</p><p><b>METHODS</b>The host animal species of hantavirus was surveyed by using the trap method and the species diversity was evaluated by using the Simpson, Shannon-Weaner, and Pielou indices. Hantavirus antigens or antibodies in lung and blood samples of all the captured host animals were detected by direct or indirect immunofluorescence.</p><p><b>RESULTS</b>Nine animal species of hantavirus were distributed in the forest ecosystem of Jiuhua Mountain. Of these, Niviventer confucianus and Apodemus agrarius were predominant, and N. confucianus, Rattus norvegicus, and Mus musculus had relatively large niche breadth index values. The host animals in the eastern and western mountain regions shared similar biodiversity index characteristics, predominant species, and species structures. Hantavirus was detected in 5 host animal species in Jiuhua Mountain area, the carriage rate of hantavirus was 6.03%. The average density of host animals in forest areas of the mountainous area was only 2.20%, and the virus infection rate in the healthy population was 2.33%.</p><p><b>CONCLUSION</b>The circulation of hantavirus was low in the forest areas of Jiuhua Mountain and did not pose a threat to human health.</p>