Characterization Of Biodiversity Research Articles

Is it worthy to use environmental DNA instead of scientific trawling or video survey to monitor taxa in soft-bottom habitats?

Non-extractive techniques such as video analysis are increasingly used by scientists to study marine communities instead of extractive methods such as trawling. Currently, environmental DNA (eDNA) analysis is seen as a revolutionary tool to study taxonomic diversity. We aimed to determine which method is the most appropriate to describe fish and commercial invertebrate diversity comparing bottom trawl hauls, video transects and seawater eDNA. Our results reveal that video detected the lowest number of taxa and trawling the highest. eDNA analysis is powerful to describe marine bony fish communities, but some taxa of importance for the ecosystem such as elasmobranchs, crustaceans or molluscs are poorly detected. This may be due to several factors such as marker specificity, incomplete reference gene databases or low DNA release in the environment. For now, the various methods provide different information and none is exhaustive enough to be used alone for biodiversity characterisation.

A diversity of diversities: Do complex environmental effects underpin associations between below‐ and above‐ground taxa?

Abstract To predict how biodiversity will respond to global change, it is crucial to understand the relative roles of abiotic drivers and biotic interactions in driving associations between the biodiversity of disparate taxa. It is particularly challenging to understand diversity–diversity links across domains and habitats, because data are rarely available for multiple above‐ and below‐ground taxa across multiple sites. Here, we analyse data from a unique biodiversity data set gathered across a variety of oceanic temperate terrestrial habitats in Wales, comprising 300 sites with co‐located soil microbial, plant, bird and pollinator surveys along with climate and soil physicochemical information. Soil groups are analysed using metabarcoding of the 16S, ITS1 and 18S DNA regions, allowing in‐depth characterisation of microbial and soil animal biodiversity. We explore biodiversity relationships along three aspects of community composition: First, we assess correlation between the alpha diversity of different groups. Second, we assess whether biotic turnover between sites is correlated across different groups. Finally, we investigate the co‐occurrence of individual taxa across sites. In each analysis, we assess the contribution of linear or nonlinear environmental effects. We find that a positive correlation between alpha diversity of plants, soil bacteria, soil fungi, soil heterotrophic protists, bees and butterflies is in fact driven by complex nonlinear responses to abiotic drivers. In contrast, environmental variation did not account for positive associations between the diversity of plants and both birds and AM fungi, suggesting a role for biotic interactions. Both the diversity and taxon‐level associations between the differing soil groups remained even after accounting for nonlinear environmental gradients. Above‐ground, spatial factors played larger roles in driving biotic communities, while linear environmental gradients were sufficient to explain many group‐ and taxon‐level relationships. Synthesis. Our results show how nonlinear responses to environmental gradients drive many of the relationships between plant biodiversity and the biodiversity of above‐ and below‐ground biological communities. Our work shows how different aspects of biodiversity might respond nonlinearly to changing environments and identifies cases where management‐induced changes in one community could either influence other taxa or lead to loss of apparent biological associations.

Characterization of biodiversity and meat quality in Guizhou yellow cattle: Correlations among intrinsic factors

This study aimed to characterize meat quality diversity among Guizhou yellow cattle and investigate the correlations among intrinsic factors that affect beef quality. Various cuts including chuck roll, fore shank, topside, rib fingers, flank, brisket, and tenderloin were taken from the carcass of Sinan cattle, Guanling cattle, and the Simmental-Guanling crossbred cattle for meat quality comparisons. The results showed that meats of all three breeds displayed high water-holding capacity and desirable meat colors, but they were tough in texture. Variations among the breeds were identified, with Guanling cattle having darker meat than the crossbred cattle. The crossbreed had lower shear force indicating potential heterosis benefits, and possessed higher fat content. Guizhou yellow cattle were leaner and more abundant in protein and umami amino acids, potentially contributing to favorable flavor. The hierarchical cluster analysis and nutritional indices assessment implicated that the composition of fatty acids demonstrated a breed-specific effect in Guanling cattle, offering greater benefits in cardiovascular disease prevention. The increased quantity of vitamin A present in the majority of cuts from crossbred and Sinan cattle enhanced their nutritional value. By multivariate data analysis, we found that as the variations in physicochemical properties increased, the nutrient compositions in beef became more complex. Overall, this study demonstrated that meats from all three breeds were nutrient-balanced high-quality protein sources, although certain indexes may vary across cuts and breeds. These variations should be considered when developing breeding strategies in the future.

Characterization of Natural Ecosystems, Biodiversity, Socioeconomic and Infrastructures for Sustainable Tourism in the National Park of Tazekka in Taza Province (Morocco)

Characterization of Natural Ecosystems, Biodiversity, Socioeconomic and Infrastructures for Sustainable Tourism in the National Park of Tazekka in Taza Province (Morocco)

The Characterization of Biodiversity and Soil Emission Activity of the “Ladoga” Carbon-Monitoring Site

The global climate crisis forces mankind to develop carbon storage technologies. “Ladoga” carbon monitoring site is part of the Russian climate project “Carbon Supersites”, which aims to develop methods and technologies to control the balance of greenhouse gases in various ecosystems. This article shows the condition of soil and vegetation cover of the carbon polygon “Ladoga” using the example of a typical southern taiga ecosystem in the Leningrad region (Russia). It is revealed that soils here are significantly disturbed as a result of agrogenic impact, and the vegetation cover changes under the influence of anthropogenic activity. It has been found that a considerable amount of carbon is deposited in the soils of the carbon polygon; its significant part is accumulated in peat soils (60.0 ± 19.8 kg × m−2 for 0–100 cm layer). In agrogenically disturbed and pristine soils, carbon stocks are equal to 12.8 ± 2.9 kg × m−2 and 8.3 ± 1.3 kg × m−2 in the 0–100 cm layer, respectively. Stocks of potentially mineralizable organic matter (0–10 cm) in peat soils are 0.48 ± 0.01 kg × m−2; in pristine soils, it is 0.58 ± 0.06 kg × m−2. Peat soils are characterized by a higher intensity of carbon mineralization 9.2 ± 0.1 mg × 100 g−1 × day−1 with greater stability. Carbon in pristine soils is mineralized with a lower rate—2.5 ± 0.2 mg × 100 g−1 × day−1. The study of microbial diversity of soils revealed that the dominant phyla of microorganisms are Actinobacteria, Bacteroidetes, and Proteobacteria; however, methane-producing Archaea—Euryarchaeota—were found in peat soils, indicating their potentially greater emission activity. The results of this work will be useful for decision makers and can be used as a reference for estimating the carbon balance of the Leningrad region and southern taiga boreal ecosystems of the Karelian Isthmus.

Isolation, characterization, and screening of yeast biodiversity for multi- hydrolytic enzymes

The current investigation was conducted with the objective of identifying yeasts that possess the ability to secrete a range of hydrolytic enzymes. Yeast isolates were collected from various samples, and the morphological characteristics of both the colony and yeast cells were examined. The capacity for enzyme production was assessed in multiple isolates by inoculating them in different media and quantifying their activities in terms of pectinase, amylase, urease, lipase, β-galactosidase, and protease. Out of a total of 42 yeast isolates, 30 displayed enzymatic activity. It is plausible that the yeast isolates obtained in this study hold potential for the production of industrial enzymes. Molecular identification techniques were employed to identify two isolates that exhibited multi-enzyme production and the highest enzyme activities. It was determined that these isolates belonged to two genera of yeasts, namely Pichia and Hanseniaspora. Specifically, isolate Y 16 was identified as Pichia kudriavizvii OL621856, while isolate Y 26 was identified as Hanseniaspora guillermondii OL621857 strains.

Tropical Mountain Peatlands from Southern Espinhaço Range, Brazil: Ecosystem Services, Biodiversity and Paleoenvironmental Reconstruction

Peatlands are transition ecosystems between terrestrial and aquatic environments, formed over time and space by the accumulation of plant materials under conditions of excessive moisture, low nutrient availability, low pH and oxygen scarcity, in which organic matter undergoes slow processes of humification. Peatland ecosystems from the Southern Espinhaço Range (SdEM), located in the State of Minas Gerais, were formed by the sui generis combination of environmental factors, setting the stage for their vast biodiversity, endemic and peculiar. For thousands of years these ecosystems have been developing, preserving proxies for environmental reconstitution, sequestering more and more carbon, and increasing their capacity to store water (spongelike effect) and regulate the water discharge from streams. Environmental reconstruction studies carried out in these ecosystems have revealed various regional paleoclimatic changes in the last 35,000 years. The carbon stock sequestered is 8.7 Mt, and 255 million m3 of water are stored in 25,385 hectares of these peatlands. These ecosystems constitute the headwaters of the most important rivers in Eastern Brazil: the São Francisco, Jequitinhonha, and Doce River basins, and regulate their flows during the dry season. However, peatlands located outside of conservation units are threatened by human activity. The Long-Term Ecological Research Program “Peatlands of the Southern Espinhaço Range: Ecosystem Services and Biodiversity” (PELDturf; funded by National Council of Scientific and Technologic Development - CNPq and Minas Gerais State Research Support Foundation - Fapemig), initiated in 2021, has intensified the characterization and monitoring of biodiversity and ecosystem services of peatlands. The results of two decades of research have revealed the importance of these ecosystems for biodiversity, the global carbon cycle, regional water resources, and paleoenvironmental reconstruction. It has also become evident that the rapid degradation of these ecosystems, mainly caused by human activity, can irreversibly compromise their ecosystem services, biodiversity, and paleoenvironmental reconstruction studies in the medium term. Therefore, it is imperative to empower local and regional communities regarding the importance of peatland ecosystems for the environment, socio-economy, and quality of life for their populations, as well as for the planet.

Distribution of rhodolith beds and their functional biodiversity characterisation using ROV images in the western Mediterranean Sea

Underwater biogenic habitats composed of unattached calcified red algae, named as rhodolith or maërl beds, may extant either alive or dead, over the seabed. The accumulation of rhodoliths constitute three-dimensional structured biogenic habitats that harbour high diversity of benthic organisms. In the Mediterranean Sea, rhodolith beds can be found between ca. 50 and 100 m, increasing diversity of the continental shelf habitats and their conservation value. Despite the remarkable relevance of these habitats, information regarding their spatial distribution in the western Mediterranean is scarce. In addition, these habitats are threatened by a range of anthropogenic activities and by climate-driven changes. In this study, we explored areas with rhodoliths' occurrence from the north to the south of the east coast of Spain. By feeding video recording data into a spatial distribution model, we assessed which biophysical drivers: (i) shape the spatial variation in the abundance of rhodoliths and (ii) define the assemblages of the biological traits and functional richness of the associated epibenthic fauna recorded by video. In addition, we examined the impact of fishing activities on these habitats. Our results evidenced that ‘Depth’ and ‘Temperature’ were important environmental factors explaining rhodoliths variation, and we defined their optimal distribution range in the western Mediterranean. The biological traits approach showed significant effects of the geographical location of rhodolith beds and their small-scale spatial heterogeneity on the functional richness index. Indeed, the lowest functional richness value was observed in the area closer to trawl fishing which could be related to habitat degradation due to trawling. This study contributes to the knowledge of deep-water rhodolith beds in the western Mediterranean and reinforce the importance of rhodolith beds in continental shelves as these constitute heterogeneous seabed habitats that harbour a high species and functional diversity.

Atlantic Oceanic Squids in the "Grey Speciation Zone".

Cryptic species complexes represent an important challenge for the adequate characterization of Earth's biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the "grey speciation zone." As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.

First insight into molecular diversity and DNA barcode library of epikarst-dwelling invertebrates in the Western Carpathians

DNA barcoding represents a handy tool for species identification. In addition, it serves as a complementary approach that improves the characterisation of evolutionary lineages and facilitates the detection of potentially undescribed and cryptic species. Based on the case study in the Western Carpathians, which belong to the Carpathian biodiversity hotspot, we have compiled the first DNA barcode reference library for molecular identification of invertebrates associated with epikarst, a unique, yet understudied, shallow subterranean aquatic habitat that extends at the interface between the soil and carbonate rocks. We analysed invertebrates collected in 2019-2020 from epikarst water that continuously seeps into four caves of the Demänovský Cave System in northern Slovakia. The standard barcode marker of the mitochondrial COI gene was amplified in more than 920 individuals of aquatic, semi-aquatic, and terrestrial invertebrates. The final data set consisted of 784 barcode sequences representing 36 morphospecies, the majority (98.3%) belonging to Arthropoda. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 60 Barcode Index Numbers (BINs), of which 43 BINs were new to BOLD, representing mostly typical subterranean species. Almost 20% of the morphospecies displayed high intraspecific variation (>2.2%), suggesting the need for further investigation to assess potential taxonomic problems or cryptic diversity. Our results also indicated the existence of several yet undescribed invertebrate species and possible heteroplasmy or COI numts in the collembolan Megalothorax sp. (incertus species group). The resulting DNA barcode library represents a significant advance not only in the characterisation of epikarst biodiversity but also in the understanding of subterranean biodiversity in general, paving the way for future complex evolutionary and biogeographical studies.

Towards Managing Biodiversity of European Marginal Agricultural Land for Biodiversity-Friendly Biomass Production

The use of marginal land, especially that which has already been used for agricultural purposes in the past two decades, for biomass cultivation is seen as an important approach for the transition to a sustainable bioeconomy. Marginal land can provide many other important ecosystem services than biomass provisioning for bioenergy and biobased products such as erosion mitigation, groundwater protection and nursery services to promote biodiversity. However, marginal land is also often subject to dynamic processes, mostly soil degradation and climate change, which make its fauna and flora particularly vulnerable to land-use changes. This study provides insights into marginal land’s potential biodiversity characterization and critically discusses further steps towards applicable management approaches. Not all commonly used indicators apply to all types of marginal land, especially regarding the site-specific biophysical constraints and the landscape heterogeneity. This is because both the biodiversity and biophysical constraints are sensitive to disturbances. Therefore, when marginal lands are used for biomass production, all available measures should be taken to allow for predominantly positive impacts on local biodiversity, such as a survey of the status quo using camera traps, area mapping, or caterpillar mimics and a forecast of potential biophysical and agrobiological impacts of management.

Diversity and ecology of molluscs (Gastropods) in mountain streams, Nurota mountain range, Uzbekistan

Abstract. Kudratov J, Pazilov A, Maxammadiyev Z, Urazova R, Otakulov B, Bazarov B, Keldiyarov K, Soatova Z, Urinova X. 2023. Diversity and ecology of molluscs (Gastropods) in mountain streams, Nurota mountain range, Uzbekistan. Biodiversitas 24: 2402-2408. Characterization of the faunal biodiversity of the regions is one of the important tasks in today's era when the influence of the anthropogenic factor has increased, and the natural ecosystems are undergoing drastic changes. Therefore, the faunal composition analysis of molluscs as a part of the natural food chain, the development of measures related to their protection, the disclosure of bioecological features, and the substantiation of scientific solutions are of great scientific and practical importance. This study provides information on the species composition of gastropod molluscs in the streams of the Nurota Mountains of Uzbekistan. Sampling was carried out at 11 stations from April to November 2019. Molluscs include 4 families (Belgrandiellidae, Lymnaeidae, Physidae and Planorbidae), 5 genera, and 15 species. The dominant family in the malacofauna of the study area is Lymnaeidae, one genus and eight species belonging to this family are found in the area. Most molluscs are found on rocky, sandy substrates around plants. This article describes the biological diversity of animals in streams in the Nurota Mountains of Uzbekistan.

About Functional Foods: The Probiotics and Prebiotics State of Art.

Poor diet, obesity and a sedentary lifestyle have a significant impact on natural microbiota disorders; specifically, the intestinal one. This in turn can lead to a multitude of organ dysfunctions. The gut microbiota contains more than 500 species of bacteria and constitutes 95% of the total number of cells in the human body, thus contributing significantly to the host's resistance to infectious diseases. Nowadays, consumers have turned to purchased foods, especially those containing probiotic bacteria or prebiotics, that constitute some of the functional food market, which is constantly expanding. Indeed, there are many products available that incorporate probiotics, such as yogurt, cheese, juices, jams, cookies, salami sausages, mayonnaise, nutritional supplements, etc. The probiotics are microorganisms that, when taken in sufficient amounts, contribute positively to the health of the host and are the focus of interest for both scientific studies and commercial companies. Thus, in the last decade, the introduction of DNA sequencing technologies with subsequent bioinformatics processing contributes to the in-depth characterization of the vast biodiversity of the gut microbiota, their composition, their connection with the physiological function-known as homeostasis-of the human organism, and their involvement in several diseases. Therefore, in this study, we highlighted the extensive investigation of current scientific research for the association of those types of functional foods containing probiotics and prebiotics in the diet and the composition of the intestinal microbiota. As a result, this study can form the foundation for a new research path based on reliable data from the literature, acting a guide in the continuous effort to monitor the rapid developments in this field.

Phenotypic biodiversity characterization of dromedary camels and hybrids in Kazakhstan.

Kazakhstan is one of the rare camel countries with rich camel biodiversity where different dromedary camels, Bactrian camels, and hybrid types are cohabiting at the same territories during centuries. Several data on phenotype biodiversity of local camels are available, mostly published during Soviet Union time using few body quantitative measurements. Unfortunately, those data are not sufficient to place the local breeds among the world camel population. The aim of this study was to describe detailed phenotype parameters of dromedary camels and hybrids in Kazakhstan and to compare our animals with the other camel populations in the world. As the whole, six camel farms were visited, located in different regions of southern Kazakhstan. In total, 185 female camels (Aruana breed camels and hybrids) were described by the phenotype questionnaire. There was a significant effect of "breed" on the different parameters except udder depth and body length. Most of the measurements were lower in Aruana compared to hybrids. The discriminating factorial analysis confirmed the clear separation between the breed based on their body measurements with a total of 95% of well-classed. The main discriminating parameters (allowing distinguishing the populations) were in the order: (i) the length of the head, (ii) the neck length, (iii) the neck circumference, (iv) the teat length, and (v) the udder length.

The Impact of Agroecological Practices on the Biodiversity of Arthropod Fauna in Târnave Vineyard


 In viticultural ecosystems, considered energy-intensive systems, the amplification of biocoenotic imbalances with the onset of pest explosions, is a problem and also an evidence of the biodiversity’s decline. In this study the biodiversity was quantified in Târnave vineyard, in the period 2016-2018, in the experimental plots of SCDVV Blaj cultivated with the Fetească regală cultivar, for two cultivation technologies, the extensive agroecological (EA) and the intensive conventional (IC). The determined biodiversity characterization indicators were: the species richness, Simpson biodiversity index (D), Shanon biodiversity index (H) and Equity index (E). In case of the Heteroptera group EA technology doubled the number of the arthropods (11.333 ± 0.882 for EA versus 5.33 ± 1.453 for IC). The reverse effect was observed for Coleoptera were in the case of EA it was found a taxa richness of 8.667 ± 0.882 and for IC one of 15.667 ± 1.764. Considering the increase of the number of useful species from the order Heteroptera in the agroecological variant compared to the conventional variant, we consider that the implementation of the agroecological technology for a longer period (5-10 years) can be a long-term solution that will contribute to reducing the risk induced by the intensive practices, while reducing the dependence of culture on conventional energy resources.

Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation

Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of biodiversity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column samples, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.

Assessment of the Genetic and Phytochemical Variability of Italian Wild Hop: A Route to Biodiversity Preservation

Background: Northern Italy has an enormous heritage of hop biodiversity that need to be exploited and studied. The preservation and valorization through the characterization of the existent biodiversity is a primary goal of the European Green Deal 2023–2030. The aim of this study was to acquire information on the biodiversity of Italian wild hops. Methods: Genetic characterization of sixty accessions was done resorting to Single Sequence Repeated (SSR) markers. Phytochemical characterization of wild hops was achieved using: (i) high-performance liquid chromatography with ultraviolet detection for bitter acids quantification, (ii) steam distillation for essential oils quantification and (iii) Gas Chromatography-Mass Spectrometry for the determination of the aromatic profile. Results: The eight SSR primers showed high Polymorphic Information Content (PIC), especially HlGA23. α-Acids reached values between 0 and 4.125. The essential oils analysis highlighted variability within the studied population, with some accessions characterized by important spicy fraction, and others by fruity and floral notes. Conclusions: The present study allowed the characterization of Italian wild hops and demonstrated an interesting biodiversity. Part of this biodiversity have been shown to be potentially suitable for use in brewing. Moreover, several genotypes could be used in breeding programs to obtain new more sustainable varieties.

Soil bacterial biodiversity characterization by flow cytometry: The bottleneck of cell extraction from soil

Abstract The importance of soil biodiversity is increasingly recognized in agriculture and natural resource research and development. Yet, traditional soil biodiversity assessments are costly and time‐consuming, limiting the extent and frequency of sampling and analysis in space and time. Flow cytometry (FCM) is a powerful technique to characterize cell communities due to its high robustness and accuracy, requiring only a short time for the characterization. Therefore, FCM could expand soil research capabilities by allowing the characterization of different aspects of bacterial biodiversity. However, this implementation of FCM requires the previous dispersion, separation and purification of bacteria from complex soil matrices. Moreover, soil monitoring programs or evaluation of soil management practices require high‐throughput analysis. In this context, soil processing protocols need to consider not only an adequate recovery of undamaged, representative and pure soil bacteria, but also short‐time processing requirements. Although soil processing protocols have been reported over time, to our knowledge, there is no recommended soil extraction protocol for high‐throughput analysis of bacterial biodiversity by FCM. We reviewed the state‐of‐art of the use of flow cytometry in scientific research and the protocols used for the extraction of bacteria from soil. We analysed the literature to take stock of the diversity of methodologies for soil processing and applications of flow cytometry in bacterial characterization considering abundance, diversity, community structure and functional properties. This review provides several lines of evidence of the use of flow cytometry for soil bacterial biodiversity (SBB) characterization, highlighting its potential for soil monitoring and studies on soil bacterial community dynamics. The review also highlights and discusses the most relevant constraints and research gaps that need to be considered for high‐throughput analysis of SBB by FCM, such as evaluation of scale‐down, new reagents for and methods of purification, threshold of bacterial recovery efficiency and selection of a standardized and validated protocol. We proposed a protocol for soil bacterial extraction for high‐throughput analysis of SBB by FCM and we provided detailed databases of systematized information that would be useful to the scientific community.

Aerobic spore-forming bacteria in powdered infant formula: Enumeration, identification by MALDI-TOF mass spectrometry (MS), presence of toxin genes and rpoB gene typing

This study aimed to assess the counts and biodiversity characterization of aerobic sporeforming bacteria (ASB) in powdered infant formula (PIF). Fifty-four (n = 54) samples of PIF of three brands were analyzed for mesophilic aerobic bacteria, and ASB counts. ASB isolated from PIF were assessed for their ability to produce spoilage enzymes and hemolytic activity and further identified by MALDI-TOF mass spectrometry. Then, the isolates were subjected to rpoB gene typing and assessment of bceT, entFM, nhe (A, B, C), and hbl (A, B, C) toxin genes. The main species isolated were B. licheniformis (54%), followed by B. cereus (33%) and B. subtilis (5%). The ASB counts ranged from 1 to 4 log CFU/g, and the mean was 2.9 log CFU/g for mesophilic aerobic sporeforming bacteria (MSC) and 2.5 log CFU/g for thermophilic aerobic sporeforming bacteria (TSC). Most PIF samples presented MSC and TSC counts between 2 and 3 log CFU/g. A total of 13%, 50%, and 37% of the samples presented MSC counts from <2 log CFU/g, between 2 and 3 log CFU/g and between 3 and 4 log CFU/g, respectively. Among the ASB isolates, 97% had protease, 84% hydrolyzed starch, 66% had hemolytic activity, and 61% had lecithinase activity. A total of 44 out of 120 isolates harbored at least one toxin gene; 56% for B. cereus, 34% for B licheniformis, and less than 5% for B. subtilis, B pumilus, and L. sphaericus. All B. cereus isolates harbored the nhe gene, 60% entFM, 44% cytK, 32% bceT, and 28% hbl genes. Besides, 17% of B. licheniformis harbored nhe. A small proportion of B. subtilis, B. pumilus, and L. sphaericus carried toxin genes. The rpoB based phylogenetic tree provided high resolution among Bacillus species. The findings of this study provide insights into the phenotypic and genotypic biodiversity of Bacillus present in PIF.

Rapid assessment of plant diversity using MODIS biophysical proxies

The spectral information derived from satellite data provides important inputs for assessing plant diversity. If a suitable satellite-derived biophysical proxy is applicable to assess and monitor plant diversity of different biogeographic regions will be of interest to policy makers and conservationists. We selected four biogeographic regions of India, i.e., semi-arid, Eastern Ghats, Western Ghats, and Northeast as the test sites on the basis of variations in moisture availability. The flora data collected for the study sites are the extract of the national biodiversity project ‘Biodiversity Characterization at Landscape Level’. The available Moderate Resolution Imaging Spectroradiometer (MODIS)-derived biophysical proxies at high temporal frequencies was considered to compare the biophysical proxies: surface reflectance-red and near-infrared, normalized difference vegetation index-NDVI, enhanced vegetation index-EVI, leaf area index-LAI, and fraction of absorbed photosynthetically active radiation-FAPAR at different temporal scales (monthly, post-monsoon, seasonal, annual) in each selected biogeographic regions of India. Generalized linear model (GLM) and multivariate adaptive regression spline (MARS) were utilized to evaluate the relationship between plant diversity and MODIS-derived biophysical proxies. MARS summarized the suitable biophysical proxies at monthly scale in descending order for the total forest area in semi-arid was red, NDVI, and FAPAR; for Eastern Ghats was EVI, FAPAR, and LAI; for Western Ghats was EVI, LAI, and FAPAR; and for Northeast was NDVI, near-infrared, and red. Furthermore, monthly FAPAR commonly found to be the suitable proxy to large scale monitoring of plant diversity in the moisture-varied biogeographic regions of India, except Northeast. Using artificial neural network, the relationship of plant diversity and monthly FAPAR/NDVI were modeled. The correlation between the predicted and reference plant diversity was found to be r = 0.56 for semi-arid, r = 0.52 for Eastern Ghats, r = 0.52 for Western Ghats and r = 0.61 for Northeast at p-value < 0.001. The study affirms that FAPAR is potentially an essential biodiversity variable (EBV) for carrying out rapid/indicative assessment of plant diversity in different biogeographic regions, and thereby, meeting various international commitments dealing with conservation and management measures for biodiversity.