Moso Bamboo Invasion Reshapes Community Structure of Denitrifying Bacteria in Rhizosphere of Alsophila spinulosa

The uncontrolled invasion of moso bamboo (Phyllostachys pubescens) dramatically alters soil nitrogen cycling and destroys the natural habitat of Alsophila spinulosa. Nevertheless, no clear evidence points out the role of denitrifying bacteria in the invasion of bamboo into the habitat of A. spinulosa. In the present study, we found that low (importance value 0.0008), moderate (0.6551), and high (0.9326) bamboo invasions dramatically altered the underground root biomass of both P. pubescens and A. spinulosa. The root biomass of A. spinulosa was maximal at moderate invasion, indicating that intermediate disturbance might contribute to the growth and survival of the colonized plant. Successful bamboo invasion significantly increased rhizospheric soil available nitrogen content of A. spinulosa, coupled with elevated denitrifying bacterial abundance and diversity. Shewanella, Chitinophaga, and Achromobacter were the primary genera in the three invasions, whereas high bamboo invasion harbored more denitrifying bacteria and higher abundance than moderate and low invasions. Further correlation analysis found that most soil denitrifying bacteria were positively correlated with soil organic matter and available nitrogen but negatively correlated with pH and water content. In addition, our findings illustrated that two denitrifying bacteria, Chitinophaga and Sorangium, might be essential indicators for evaluating the effects of bamboo invasion on the growth of A. spinulosa. Collectively, this study found that moso bamboo invasion could change the nitrogen cycling of colonized habitats through alterations of denitrifying bacteria and provided valuable perspectives for profound recognizing the invasive impacts and mechanisms of bamboo expansion.

Diversity and time-series analyses of Caribbean deep-sea coral and sponge assemblages on the tropical island slope of Isla de Roatán, Honduras

Shore-based submersible operations, from 2006 to 2020, have allowed us to examine megabenthic assemblages along the island margin of Isla de Roatán from depths of about 150 to 750 m, including repeated observations of the same organisms. These dives were used to photo-document a diverse benthic assemblage and observe the health and condition of the sessile fauna in a well-explored but relatively undocumented area of the Mesoamerican Reef. Samples were collected by dip net, and some dives profiled the water column chemistry in the year 2011. The deep-sea coral assemblage observed off Roatan exhibits high abundance and diversity. The sessile habitat-forming taxa consist primarily of at least 20 different octocorals (e.g., Plexauridae, Primnoidae, Coralliidae, Isididae, and Ellisellidae) and 20 different sponges each (Demospongiae and Hexactinellida), with several known and unknown taxa of Zoantharia, Antipatharia (Bathypathes spp), and Scleractinia (e.g., Desmophyllum pertusum, Dendrophyllia alternata, Madracis myriaster, and solitary taxa). Crinoidea were also abundant and diverse, represented by at least nine species. Epifaunal assemblages associated with corals include at least 24 macroinvertebrate species dominated by Asteroschema laeve (Ophiuroidea) and Chirostylus spp. (Decapoda: Anomura). Repeated observations of a few large octocoral colonies over many years illustrate patterns of predation, recolonization, and epibiont host fidelity, including a 14-year record of decline in a plexaurid octocoral (putatively Paramuricea sp.) and loss of its resident ophiuroids. The shore-based submersible provides a practical and relatively inexpensive platform from which to study coral and sponge assemblages on a deep tropical island slope. The deep-sea coral gardens are likely to harbor new species and new discoveries if more samples can be acquired and made available for taxonomic research.

HPLC and high-throughput sequencing revealed differences of tea-leaves quality components and soil microbial community structure between modern and ancient tea plantations in Lincang Region

BackgroundAncient tea plantations with an age over 100 years still reserved at Mengku Town in Lincang Region of Yunan Province, China. However, the characteristic of soil chemicophysical properties and microbial ecosystem in the ancient tea plantations and their impact on tea-leaves chemical components remained unclear. Tea-leaves chemical components including amino acids, phenolic compounds and purine alkaloids, and soil chemicophysical properties including pH, cation exchange capacity (CEC), soil organic matter (SOM), soil organic carbon (SOC), total total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkali-hydrolyzable nitrogen (AN), available phosphorous (AP) and available potassium (AK), and microbial community structure of modern and ancient tea plantations in five geographic sites (i.e. Bingdao, Baqishan, Banuo, Dongguo and Jiulong) were determined by high performance liquid chromatography (HPLC) and high-throughput sequencing, respectively. ResultsTea-leaves chemical components, soil chemicophysical properties and microbial community structures including bacterial and fungal community abundance and diversity evaluated by Chao 1 and Shannon varied with geographic location and tea plantation type. The ancient tea plantations possessed significantly (P<0.05) higher free amino acids, gallic acid, caffeine and EGC in tea-leaves, as well as soil fertility. The bacterial community structure kept stable, while fungal community abundance and diversity significantly (P<0.05) increased in ancient tea plantation because of higher soil fertility and lower pH. The long-term plantation in natural cultivation way significantly (P<0.05) improved the abundances of Nitrospirota, Methylomirabilota, Ascomycota and Mortierellomycota phyla. ConclusionsDue to the natural cultivation way, the ancient tea plantations still maintained relatively higher soil fertility and complete soil microbial ecosystem, which contributed to the sustainable development with higher quality in tea-leaves.

The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs

Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, Prevotella 7, Syntrophococcus, Sharpea, Dialister, Pseudoscardovia, and Megasphaera in the rumen of the EW group had greater relative abundances. At 35 d, the Lachnospiraceae_NK3A20_group was enriched in CON. On 63 d, Erysipelotrichaceae_UCG-002 was abundant in EW. Syntrophococcus and Megaspheaera in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of Erysipelotrichaceae_UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of Syntrophococcus, Megasphaera, and Ruminococcaceae_UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning.

The impact of reduced tillage and distance to field margin on predator functional diversity

Introduction Agricultural intensification results in biodiversity loss through land conversion and management practices which negatively impact arthropods. The abundance and diversity of ground-dwelling predators, e.g. ground beetles (Coleoptera: Carabidae) and spiders (Araneae), are negatively affected by soil disturbances such as tillage. Reducing soil disturbances can potentially conserve arthropod populations in the field and reduce the use of chemical pest controls. The present study investigated the ground-dwelling predatory community using pitfall traps in cereal fields with three different levels of soil disturbance: conventional tillage, reduced tillage and no tillage under Conservation Agriculture management, in 2018 and 2019. Pitfall traps were placed in transects from the field margins. Overall, the activity-density of ground-dwelling predators was higher in fields with minimum soil disturbance and generally declined with increased distance to semi-natural habitats. Functional diversity, expressed by the body size of ground beetles, was also affected by soil disturbances; large ground beetles more consistently occurred in CA, while few or none of the largest ground beetles were found in RT and CT. A higher sample-heterogeneity in less disturbed fields was indicated by a more variable median and higher skewness in the number of predators in those fields. In 2019 only, species diversity was higher along field edges bordering semi-natural habitats when compared to the cropped area. Our results show that reduced tillage supports predator arthropod communities at a local scale: It also bolsters agro-ecosystem resilience by promoting a higher activity-density and by increasing the heterogeneity and functional diversity of ground-dwelling predators. Implications for insect conservation The results obtained in the present study show that soil disturbances significantly influence arthropod abundance and diversity. Conservation of epigeic natural enemies in the agricultural landscape is improved by reducing soil-disturbing events such as tillage.

Diversity and abundance of some insect fauna in Bhawal and Madhupur Sal forests of Bangladesh

The abundance and diversity of insect fauna were studied from two deciduous sal forests of Bhawal and Madhupur located at central part of Bangladesh. A total of 544 individuals of insects of 61 species belonging to 54 genera, 33 families and 11 orders have been identified with Hymenoptera (31%) as the dominant order in species richness followed by Coleoptera (13%), Orthoptera (11%), Diptera (10%), Hemiptera (8%), Lepidoptera (8%), Odonata (8%), Homoptera (3%), Isoptera (3%), Neuroptera (3%) and Dictyoptera (2%). Bhawal scores higher Shannon-Weaver diversity index (Hʹ=3.725) compared to Madhupur (Hʹ=3.340). The Bhawal Sal Forest with the collected 341 (63%) insects and identified 53 (59%) species belonging to 10 orders was found more diverse in species richness than the Madhupur Sal Forest with 37(41%) species belonging to 11 orders identified from the collected 203 (37%) insect samples. Insects of the order Neuroptera were not recorded from Bhawal. Off the 61 species, 29(48%) species were common in both the forests, 24(39%) species were exclusive to Bhawal and eight (13%) species were exclusive to the Madhupur Sal Forest. Apis cerana of Hymenoptera was identified as the dominant species having 9% of the identified samples followed by dipteran species Musca domestica with 6% of the samples. Among the insect species 30 (49%) species were found playing beneficial role as biological control agents, predators, pollinators, honey producers and also organic debris recycler. On the other hand, 31(51%) species were found to be harmful causing damage to forest vegetation as well as human and wildlife at variable degrees. J. Biodivers. Conserv. Bioresour. Manag. 2021, 7(1): 11-24

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf

Throughout coastal Antarctica, ice shelves separate oceanic waters from sunlight by hundreds of meters of ice. Historical studies have detected activity of nitrifying microorganisms in oceanic cavities below permanent ice shelves. However, little is known about the microbial composition and pathways that mediate these activities. In this study, we profiled the microbial communities beneath the Ross Ice Shelf using a multi-omics approach. Overall, beneath-shelf microorganisms are of comparable abundance and diversity, though distinct composition, relative to those in the open meso- and bathypelagic ocean. Production of new organic carbon is likely driven by aerobic lithoautotrophic archaea and bacteria that can use ammonium, nitrite, and sulfur compounds as electron donors. Also enriched were aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates, likely derived from in situ fixed carbon and potentially refractory organic matter laterally advected by the below-shelf waters. Altogether, these findings uncover a taxonomically distinct microbial community potentially adapted to a highly oligotrophic marine environment and suggest that ocean cavity waters are primarily chemosynthetically-driven systems.

Intestinal Taxa Abundance and Diversity in Inflammatory Bowel Disease Patients: An Analysis including Covariates and Confounders

Intestinal dysbiosis has been widely documented in inflammatory bowel diseases (IBDs) and is thought to influence the onset and perpetuation of gut inflammation. However, it remains unclear whether such bacterial changes rely in part on the modification of an IBD-associated lifestyle (e.g., smoking and physical activity) and diet (e.g., rich in dairy products, cereals, meat and vegetables). In this study, we investigated the impact of these habits, which we defined as confounders and covariates, on the modulation of intestinal taxa abundance and diversity in IBD patients. 16S rRNA gene sequence analysis was performed using genomic DNA extracted from the faecal samples of 52 patients with Crohn’s disease (CD) and 58 with ulcerative colitis (UC), which are the two main types of IBD, as well as 42 healthy controls (HC). A reduced microbial diversity was documented in the IBD patients compared with the HC. Moreover, we identified specific confounders and covariates that influenced the association between some bacterial taxa and disease extent (in UC patients) or behaviour (in CD patients) compared with the HC. In particular, a PERMANOVA stepwise regression identified the variables “age”, “eat yogurt at least four days per week” and “eat dairy products at least 4 days per week” as covariates when comparing the HC and patients affected by ulcerative proctitis (E1), left-sided UC (distal UC) (E2) and extensive UC (pancolitis) (E3). Instead, the variables “age”, “gender”, “eat meat at least four days per week” and “eat bread at least 4 days per week” were considered as covariates when comparing the HC with the CD patients affected by non-stricturing, non-penetrating (B1), stricturing (B2) and penetrating (B3) diseases. Considering such variables, our analysis indicated that the UC extent differentially modulated the abundance of the Bifidobacteriaceae, Rikenellaceae, Christensenellaceae, Marinifilaceae, Desulfovibrionaceae, Lactobacillaceae, Streptococcaceae and Peptostreptococcaceae families, while the CD behaviour influenced the abundance of Christensenellaceae, Marinifilaceae, Rikenellaceae, Ruminococcaceae, Barnesiellaceae and Coriobacteriaceae families. In conclusion, our study indicated that some covariates and confounders related to an IBD-associated lifestyle and dietary habits influenced the intestinal taxa diversity and relative abundance in the CD and UC patients compared with the HC. Indeed, such variables should be identified and excluded from the analysis to characterize the bacterial families whose abundance is directly modulated by IBD status, as well as disease extent or behaviour.

Local Environmental Conditions Promote High Turnover Diversity of Benthic Deep-Sea Fungi in the Ross Sea (Antarctica)

Fungi are a ubiquitous component of marine systems, but their quantitative relevance, biodiversity and ecological role in benthic deep-sea ecosystems remain largely unexplored. In this study, we investigated fungal abundance, diversity and assemblage composition in two benthic deep-sea sites of the Ross Sea (Southern Ocean, Antarctica), characterized by different environmental conditions (i.e., temperature, salinity, trophic availability). Our results indicate that fungal abundance (estimated as the number of 18S rDNA copies g−1) varied by almost one order of magnitude between the two benthic sites, consistently with changes in sediment characteristics and trophic availability. The highest fungal richness (in terms of Amplicon Sequence Variants−ASVs) was encountered in the sediments characterized by the highest organic matter content, indicating potential control of trophic availability on fungal diversity. The composition of fungal assemblages was highly diverse between sites and within each site (similarity less than 10%), suggesting that differences in environmental and ecological characteristics occurring even at a small spatial scale can promote high turnover diversity. Overall, this study provides new insights on the factors influencing the abundance and diversity of benthic deep-sea fungi inhabiting the Ross Sea, and also paves the way for a better understanding of the potential responses of benthic deep-sea fungi inhabiting Antarctic ecosystems in light of current and future climate changes.