Greater Shannon Diversity Research Articles

Microbiome ecological memory and responses to repeated marine heatwaves clarify variation in coral bleaching and mortality.

Microbiomes are essential features of holobionts, providing their hosts with key metabolic and functional traits like resistance to environmental disturbances and diseases. In scleractinian corals, questions remain about the microbiome's role in resistance and resilience to factors contributing to the ongoing global coral decline and whether microbes serve as a form of holobiont ecological memory. To test if and how coral microbiomes affect host health outcomes during repeated disturbances, we conducted a large-scale (32 exclosures, 200 colonies, and 3 coral species sampled) and long-term (28 months, 2018-2020) manipulative experiment on the forereef of Mo'orea, French Polynesia. In 2019 and 2020, this reef experienced the two most severe marine heatwaves on record for the site. Our experiment and these events afforded us the opportunity to test microbiome dynamics and roles in the context of coral bleaching and mortality resulting from these successive and severe heatwaves. We report unique microbiome responses to repeated heatwaves in Acropora retusa, Porites lobata, and Pocillopora spp., which included: microbiome acclimatization in A. retusa, and both microbiome resilience to the first marine heatwave and microbiome resistance to the second marine heatwave in Pocillopora spp. Moreover, observed microbiome dynamics significantly correlated with coral species-specific phenotypes. For example, bleaching and mortality in A. retusa both significantly increased with greater microbiome beta dispersion and greater Shannon Diversity, while P. lobata colonies had different microbiomes across mortality prevalence. Compositional microbiome changes, such as changes to proportions of differentially abundant putatively beneficial to putatively detrimental taxa to coral health outcomes during repeated heat stress, also correlated with host mortality, with higher proportions of detrimental taxa yielding higher mortality in A. retusa. This study reveals evidence for coral species-specific microbial responses to repeated heatwaves and, importantly, suggests that host-dependent microbiome dynamics may provide a form of holobiont ecological memory to repeated heat stress.

Soil organic carbon stocks and belowground biomass in patches in heterogeneous grassland

AbstractBackgroundSelective grazing creates stable patches of contrasting sward height, thereby providing different growth conditions for the grass sward above and below ground and potentially affecting soil organic carbon (SOC) stocks. We hypothesized that the presence of patches leads to greater spatial variability in belowground biomass (BGB) and SOC stocks than occurs between pastures managed under different stocking intensities.MethodsA long‐term grazing experiment consisting of three stocking intensities was used for this study. We studied BGB, SOC, and soil total nitrogen (Ntot) stocks in the 0–15 cm soil depth. Shannon diversity of plant species, soil bulk density, soil phosphorus, potassium, and magnesium contents were considered.ResultsThere were no significant effects of patch or stocking intensity on BGB, SOC, and Ntot stocks. Short patches had a greater Shannon diversity than tall patches (p < 0.05) and plant‐available nutrients in soil correlated positively with sward height (p < 0.05).ConclusionsWe conclude from the current results and previous studies that higher plant species diversity with lower soil nutrient contents in short‐patch areas and higher nutrient contents together with light competition in tall‐patch areas might balance each other out with respect to BGB and SOC stocks.

GEOGRAPHIC DISTRIBUTION AND CONSERVATION OF ANDEAN AGROBIODIVERSITY IN THE PROVINCE OF IMBABURA – ECUADOR

The ever-increasing relevancy of agrobiodiversity studies is motivated by its important role in food security, conservation, and economic value for rural communities. In order to determine geographic distribution and state of conservation of agrobiodiversity in the Andes’ highlands of the province of Imbabura – Ecuador, 606 farmers were surveyed from 85 communities located over 2,500 masl. Standard Deviational Ellipse was used to determine the trend of spatial distribution; Shannon - Weinner, Simpson, and Margalef indexes, as well as cluster analysis were used to study abundance and conservation. Inverse Distance Weighted interpolation was used to determine the trend of uses. The spatial autocorrelation Moran's I index and the ‘Near’ tool were used to define the influence of proximity to urban areas, and the correlation coefficient to establish the relationship between ethnicity and conservation. The study identified 47 species from seven different groups of crops. Most agro-biodiverse zones were located in Otavalo. Most abundant specie was corn (Zea mays), (19.11% abundance). Pimampiro has a greater Shannon diversity (H'= 1.118). Otavalo has the highest maximum diversity (Hmax = 1.602), and Urcuquí has the greatest Shannon evenness among species (J'=0.931). Highest Simpson dominance index (D= 0.15) was found in Antonio Ante. Corn has the highest number of uses. Highest levels of agrobiodiversity conservation were found in Gonzalez Suarez and Otavalo. Ethnicity and conservation showed an inverse correlation (correlation coefficient = -0.77). Agrobiodiversity conservation shows spatial autocorrelation and values show tendency to clustering (Moran’s I=0.25; z-score=2.80 and p-value=0.005). This research supports the conclusion that the most agro-biodiverse areas, with higher levels of conservation of agrobiodiversity are in Otavalo.

Exploiting the Potential of Bioreactors for Creating Spatial Organization in the Soil Microbiome: A Strategy for Increasing Sustainable Agricultural Practices

Industrial production of synthetic nitrogen fertilizers and their crop application have caused considerable environmental impacts. Some eco-friendly alternatives try to solve them but raise some restrictions. We tested a novel method to produce a nitrogen bioinoculant by enriching a soil microbial community in bioreactors supplying N2 by air pumping. The biomass enriched with diazotrophic bacteria was diluted and applied to N-depleted and sterilized soil of tomato plants. We estimated microbial composition and diversity by 16S rRNA metabarcoding from soil and bioreactors at different run times and during plant uprooting. Bioreactors promoted the N-fixing microbial community and revealed a hided diversity. One hundred twenty-four (124) operational taxonomic units (OTUs) were assigned to bacteria with a greater Shannon diversity during the reactor’s steady state. A total of 753 OTUs were found in the rhizospheres with higher biodiversity when the lowest concentration of bacteria was applied. The apparent bacterial abundance in the batch and continuous bioreactors suggested a more specific functional ecological organization. We demonstrate the usefulness of bioreactors to evidence hidden diversity in the soil when it passes through bioreactors. By obtaining the same growth of inoculated plants and the control with chemical synthesis fertilizers, we evidence the potential of the methodology that we have called directed bioprospecting to grow a complex nitrogen-fixing microbial community. The simplicity of the reactor’s operation makes its application promising for developing countries with low technological progress.

Edaphic fauna and physico-chemical atributes of soil in different phytophysionomies of Cerrado

ABSTRACT The edaphic community comprises several organisms that perform ecological functions in the environment, such as litter fragmentation, nutrient cycling, and modifications of soil structure, in addition to acting as food chain regulators. Thus, the objective of this study was to evaluate the composition of the edaphic fauna and the physical and chemical attributes of soil in different physiognomies of Cerrado in the Parque Estadual do Mirador (PEM). The study was carried out in two Cerrado formations (Sparse Cerrado and Typical Cerrado) in PEM, where 100 pitfall traps were installed. The edaphic organisms were screened and identified in terms of orders, suborders, subfamilies, families, abundance, richness, Shannon diversity, and Pielou’s equitability. A total of 4,149 individuals were collected from two experimental plots. The plot in the Typical Cerrado showed greater taxonomic richness (25 groups) and greater Shannon diversity (H’ = 1.65), while the plot in Sparse Cerrado presented 19 edaphic groups and Shannon diversity equal to H’ = 1.51. The factorial exploration explained 84.43% of the original data from the Sparse Cerrado and 90.84% from the Typical Cerrado. It is concluded that the plot in the Typical Cerrado showed greater differences in terms of richness and abundance due to the more favorable conditions for soil fauna, such as a high content of organic material and greater vegetation cover.

Microbial inoculation and fertilizer application on growth of cowpea and spore-based assemblages of arbuscular mycorrhizal fungi in its rhizophere.

In this study, the effect of microbial inoculants and fertilizer application on cowpea (BRS Pujante) growth and on the structure and composition of arbuscular mycorrhizal fungi (AMF) assemblages were evaluated. A completely randomized experiment was set up involving 17 treatments: four with AMF, three with nodulating bacteria, six with AMF + nodulating bacteria, two with phosphorus, one with nitrogen and one control (reference) in five replicates. Plant growth and nutritional content, mycorrhizal colonization, glomerospores number, spore-based AMF assemblages and ecological indices were evaluated. Mycorrhizal inoculants associated with Bradyrhizobium BR3267 strain were more effective than the Microvirga BR3296 strain. Multidimensional scaling analysis showed that Acaulospora longula treatments were more similar among themselves, and distinct from the other treatments. A difference was observed in the structure of AMF community assemblage between treatments with G. albida + Bradyrhizobium BR 3267 and A. longula, with greater Shannon diversity and Pielou equitability indices in the first treatment and greater dominance in the treatment with A. longula only. Long-term studies are required to determine if the successful establishment of A. longula among indigenous species persists over time and if its dominant behavior is not deleterious to the AMF native community.

Multifractal analysis of soil fauna diversity indexes

ABSTRACT The objective of this study was to determine the multifractality of diversity indexes of edaphic fauna in areas with natural vegetation and in agricultural systems. Biological sampling was carried out in seven treatments (millet, maize, soybean, eucalyptus, preserved cerrado, disturbed cerrado and pasture), containing 130 pitfall traps, distributed in transects with 3 m of spacing between sampling points, totaling 390 m. The multifractal analysis was determined based on the moment method, where estimates such as the capacity dimensions, entropy and the correlation of the diversity indexes were calculated. The soybean area had greater Shannon diversity (2.69), however it had smaller abundance of individuals. The partition functions were adjusted with coefficient of determination > 0.90. The difference between D-10-D10, ranged from 0.080 to 1,707 for Pielou equitability in soybean cultivation, for richness in the area under the cultivation of eucalyptus. The singularity spectra expressed graphs with different degrees of heterogeneity for the soil fauna indexes, and the richness expressed the best structure. The area cultivated with soybean had a monofractal tendency, due to the homogeneous distribution of individuals of the edaphic fauna along the transect. The fractal analysis provided the description of patterns of variability that are not detected by classical methods.

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes.

Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.

The musk chemical composition and microbiota of Chinese forest musk deer males.

Male musk deer secrete musk from the musk gland located between their naval and genitals. Unmated male forest musk deer generate a greater amount of musk than mated males, potentially allowing them to attract a greater number of females. In this study, we used gas chromatography and mass spectrometry (GC/MS) to explore musk chemical composition of the musk pods of captive mated and unmated sexually mature Chinese forest musk deer and used next-generation sequencing to intensively survey the bacterial communities within them. Analysis of the chemical composition of the musk showed that unmated males have more muscone and cholesterol. Features of the musk16S rRNA gene showed that mated Chinese forest musk deer have both a greater Shannon diversity (p < 0.01) and a greater number of estimated operational taxonomic units than unmated ones; many bacterial genera were overrepresented in unmated Chinese forest musk deer males. Members of these genera might be involved in musk odor fermentation. PICRUSt analysis revealed that metabolic pathways such as aldosterone-regulated sodium reabsorption, metabolism of terpenoids and polyketides, flavone and flavonol biosynthesis, and isoflavonoid biosynthesis were enriched in the musk of unmated Chinese forest musk deer males.

Effects of Set-aside Conservation Practices on Bird Community Structure within an Intensive Agricultural Landscape

Creating and restoring patches of noncrop early-succession vegetation within agricultural landscapes may mitigate grassland bird population declines caused by agricultural land use and intensification. Achieving this goal requires an ability to balance avian benefits with agronomics, which may be facilitated by understanding how bird communities respond to various conservation practices. We evaluated bird richness, abundance, Shannon diversity, and Total Avian Conservation Value in 20 replicates of four Conservation Reserve Program practices in an intensive rowcrop agricultural landscape in the Mississippi Alluvial Valley from May–Jul., 2005–2007. Conservation practices included: (1) large blocks of structurally-diverse early-succession vegetation (6–8 y old trees) and three buffer types; (2) 30 m wide monotypic filter strips with tall dense switchgrass (Panicum virgatum); (3) 30 m wide diverse filter strips with a forb-native warm season grass mixture; and (4) 60 m wide early-succession riparian forest buffers (1–3 y old trees). The breeding bird community was dominated by red-winged blackbirds (Agelaius phoeniceus; 43% of total) and dickcissels (Spiza americana; 42% of total) but commonly included eastern meadowlarks (Sturnella magna), indigo buntings (Passerina cyanea), mourning doves (Zenaida macroura), and northern bobwhite (Colinus virginianus). We observed ≥1.8 × more dickcissels in large blocks and diverse filter strips than other buffers and greater Shannon diversity in large blocks than any buffers (P < 0.05). Diverse filter strips had ≥1.6 × greater overall bird density (7.2 birds/0.6 ha), on average, than all other practices. Based on these data, we conclude that buffers are attractive to farmland breeding birds and may provide important ecological benefits to supplement a conservation management system founded on large blocks of early-succession vegetation.

Effect of dam parity on litter performance, transfer of passive immunity, and progeny microbial ecology1

Litter performance and progeny health status may be decreased in progeny derived from primiparous sows but improve with increasing parity. The objective was to evaluate litter performance, the production and passive transfer of Ig, and fecal microbial populations in progeny derived from first parity (P1) compared with fourth parity (P4) dams. Litter performance was recorded for P1 (n = 19) and P4 (n = 24) dams including number of pigs/litter (total born, born live, stillbirths, mummified fetuses, prewean mortality, and pigs weaned) and average litter and piglet BW at birth (d 0), d 7, d 14, and at weaning (average d 19). Blood samples were collected from all dams on d 90 and 114 of gestation and d 0 of lactation. Colostrum and milk samples were collected from each dam on d 0, 7, and 14 of lactation for quantification of IgG and IgA. Blood and fecal samples were collected from each litter (n = 6 pigs/litter) on d 1, 7, and 14 after parturition. Circulating IgG and IgA concentrations were quantified in all blood samples. Denaturing gradient gel electrophoresis (DGGE) was used to characterize similarity and diversity of fecal microbes among progeny. Progeny of P1 dams had decreased average litter BW at d 7 (25.7 vs. 30.0 kg; P < 0.03) and decreased average piglet BW throughout the experiment (d 0, 7, 14, and 19; P < 0.001) compared with P4 progeny. No parity × day interactions were observed with respect to immunoglobulin or microbial analyses. Concentrations of IgA tended to be greater (P = 0.09) in samples of colostrum and milk obtained from P4 compared with P1 dams. Serum IgG concentrations were greater (P < 0.02) in P4 progeny compared with P1 progeny. Results of DGGE revealed that P1 progeny had increased (P < 0.001) microbial similarity on d 7 and decreased (P < 0.03) microbial similarity on d 14 compared with P4 progeny. Progeny of P1 dams tended (P = 0.07) to have a greater Shannon's diversity index compared with P4 progeny on d 1, and P1 progeny had a greater (P < 0.03) Shannon's diversity index compared with P4 progeny on d 7. Litter performance, passive transfer of immunity, and progeny microbial ecology were affected by dam parity.

Biodiversity and ecological composition of macrobenthos on cold-water coral mounds and adjacent off-mound habitat in the bathyal Porcupine Seabight, NE Atlantic

The cold-water scleractinian corals Lophelia pertusa and Madrepora oculata form mound structures on the continental shelf and slope in the NE Atlantic. This study is the first to compare the taxonomic biodiversity and ecological composition of the macrobenthos between on- and off-mound habitats. Seven box cores from the summits of three mounds and four cores from an adjacent off-mound area in the Belgica Mound Province in the Porcupine Seabight yielded 349 species, including 10 undescribed species. On-mound habitat was three times more speciose, and was richer with higher evenness and significantly greater Shannon's diversity than off-mound. Species composition differed significantly between habitats and the four best discriminating species were Pliobothrus symmetricus (more frequent off-mound), Crisia nov. sp, Aphrocallistes bocagei and Lophelia pertusa (all more frequent on-mound). Filter/suspension feeders were significantly more abundant on-mound, while deposit feeders were significantly more abundant off-mound. Species composition did not significantly differ between mounds, but similarity within replicates decreased from Galway Mound<Thérèse Mound<off-mound. We propose that, despite having greater vertical habitat heterogeneity that supports higher biodiversity, coral mounds have a characteristic “reef fauna” linked to species’ biology that contrasts with the higher horizontal habitat heterogeneity conferred by the action of deposit feeders and a varied seabed sedimentary facies off-mound. Standardisation of equipment and restriction of analyses to higher taxonomic levels would facilitate prospective comparative analyses of cold-water coral biodiversity across larger spatio–temporal scales.