Effects of long-term floodplain disconnection on multiple facets of lake fish biodiversity: Decline of alpha diversity leads to a regional differentiation through time

Abstract Cross talk between the intestinal microbiome and the lung and its role in lung health remains unknown. Perinatal exposure to antibiotics disrupts the neonatal microbiome and may have an impact on the preterm lung. We hypothesized that perinatal antibiotic exposure leads to long-term intestinal dysbiosis and increased alveolar simplification in a murine hyperoxia model. Pregnant C57BL/6 wild type dams and neonatal mice were treated with antibiotics before and/or immediately after delivery. Control mice received phosphate-buffered saline (PBS). Neonatal mice were exposed to 95% oxygen for 4 days or room air. Microbiome analysis was performed using 16S rRNA gene sequencing. Pulmonary alveolarization and vascularization were analyzed at postnatal day (PND) 21. Perinatal antibiotic exposure modified intestinal beta diversity but not alpha diversity in neonatal mice. Neonatal hyperoxia exposure altered intestinal beta diversity and relative abundance of commensal bacteria in antibiotic treated mice. Hyperoxia disrupted pulmonary alveolarization and vascularization at PND 21; however, there were no differences in the degree of lung injury in antibiotic treated mice compared to vehicle treated controls. Our study suggests that exposure to both hyperoxia and antibiotics early in life may cause long-term alterations in the intestinal microbiome, but intestinal dysbiosis may not significantly influence neonatal hyperoxic lung injury.

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The long-term conservation of forest diversity in New Zealand

Pacific Conservation Biology ◽

10.1071/pc950077 ◽

1995 ◽

Vol 2 (1) ◽

pp. 77 ◽

Cited By ~ 16

Author(s):

John Ogden

Keyword(s):

New Zealand ◽

Land Surface ◽

Alpha Diversity ◽

Forest Diversity ◽

Forest Reserves ◽

Introduced Plants ◽

Wide Range ◽

Average Loss ◽

Endemic Flora

The largely endemic flora of New Zealand is a remnant of the Cretaceous flora of Gondwana, supplemented by later additions from Australia and the tropics. Semi-natural plant communities cover about 50% of the country, and a scheme for the protection of supposedly representative areas is in place. Existing reserves do not adequately reflect the patterns of plant species diversity. Many are modified by introduced animals and alien plants. The latter are being actively introduced into New Zealand at the rate of c. 11 species per year. Measures of diversity are discussed and the broad pattern of (gamma) diversity and endemicity in the country is described. A comparison is made between (alpha) diversity levels in Beech Nothofagus solandri var. cliffortioidesand Kauri Agathis australisforest. Within each of these two forest types there are similar levels of alpha-diversity over a wide range of latitude. Altitudinal alpha-diversity trends indicate an average loss of 3.4 species per 100 m of altitude. This can be accounted for by the reduction of land surface area with increasing altitude on conical or ridge-shaped mountains. The altitudinal data emphasize the importance of the lowlands in the conservation of bio-diversity. The Holocene history of the forests in New Zealand suggests that the concept of "representativeness" is flawed: forest varies continuously in time and space. It may be possible to create some "living museums" of the past biota of New Zealand, but unless there are radical changes in our ability to eradicate animal pests and introduced plants, the composition of mainland forest reserves in the lowlands will change dramatically over the next few centuries. Conservation effort on saving endangered birds may have been at the expense of long-term "habitat" survival on the mainland.

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Continuities and discontinuities of Russian urban housing: The Soviet housing experiment in historical long-term perspective

Urban Studies ◽

10.1177/0042098019852326 ◽

2019 ◽

Vol 57 (8) ◽

pp. 1768-1785 ◽

Cited By ~ 2

Author(s):

Alexander Kalyukin ◽

Sebastian Kohl

Keyword(s):

Urban Housing ◽

Regional Differentiation ◽

Differential Growth ◽

Living Space ◽

Housing Characteristics ◽

Per Capita ◽

Soviet Legacy ◽

Almost All ◽

Over Time

Did the socialist experiment disrupt continuity in Russian urban housing? Based on a unique collection of urban data covering several hundred Russian cities and spanning three regimes across more than a century, this paper gives a nuanced account of continuities and discontinuities of housing in post-Soviet cities. Three main housing characteristics are analysed: urban density (persons per building and living space per capita), ownership structure and the modernisation of stock (building material and provision with amenities). Although all Russian cities underwent a number of major shocks and regime changes during the course of the 20th century, their rankings with regard to these three key housing characteristics are still significantly correlated over time, whereas living space per capita is largely uncorrelated over time. This holds true despite significant convergence processes in almost all dimensions and also when including contemporary control variables. We hypothesise that local or regional building traditions, regional differentiation in Soviet urban planning as well as Soviet land use specificities could explain differential growth across cities. Going beyond existing late-Soviet-legacy timeframes, the long-term perspective reveals that even major regime shocks did not completely erase regionally shaped patterns in housing conditions.

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Differential responses of arbuscular mycorrhizal fungal communities to long-term fertilization in the wheat rhizosphere and root endosphere

Applied and Environmental Microbiology ◽

10.1128/aem.00349-21 ◽

2021 ◽

Author(s):

Yuying Ma ◽

Huanchao Zhang ◽

Daozhong Wang ◽

Xisheng Guo ◽

Teng Yang ◽

...

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Rhizosphere Soil ◽

Organic Amendments ◽

Alpha Diversity ◽

Arbuscular Mycorrhizal ◽

Mineral Fertilization ◽

Amf Communities ◽

Arbuscular Mycorrhizal Fungal

Arbuscular mycorrhizal fungi (AMF) provide essential nutrients to crops and are critically impacted by fertilization in agricultural ecosystems. Understanding shifts in AMF communities in and around crop roots under different fertilization regimes can provide important lessons for improving agricultural production and sustainability. Here, we compared the responses of AMF communities in the rhizosphere (RS) and root endosphere (ES) of wheat ( Triticum aestivum ) to different fertilization treatments: Non-fertilization (Control), mineral fertilization only (NPK), mineral fertilization plus wheat straw (NPKS), and mineral fertilization plus cow manure (NPKM). We employed high-throughput amplicon sequencing and investigated the diversity, community composition, and network structure of AMF communities to assess their responses to fertilization. Our results elucidated that AMF communities in the RS and ES respond differently to fertilization schemes. Long-term NPK application decreased the RS AMF alpha diversity significantly, whereas additional organic amendments (straw or manure) had no effect. Contrastingly, NPK fertilization increased the ES AMF alpha diversity significantly, while additional organic amendments decreased it significantly. The effect of different fertilization schemes on AMF network complexity in the RS and ES were similar to their effects on alpha diversity. Changes to AMF communities in the RS and ES correlated mainly with the pH and phosphorus level of the rhizosphere soil under long-term inorganic and organic fertilization regimes. We suggest that the AMF community in the roots should be given more consideration when studying the effects of fertilization regimes on AMF in agroecosystems. Importance Arbuscular mycorrhizal fungi are an integral component of rhizospheres, bridging the soil and plant systems and are highly sensitive to fertilization. However, surprisingly little is known about how the response differs between the roots and the surrounding soil. Decreasing arbuscular mycorrhizal fungal diversity under fertilization has been reported, implying a potential reduction in the mutualism between plants and arbuscular mycorrhizal fungi. However, we found opposing responses to long-term fertilization managements of arbuscular mycorrhizal fungi in the wheat roots and rhizosphere soil. These results suggested that changes in the arbuscular mycorrhizal fungal community in soils do not reflect those in the roots, highlighting that the root arbuscular mycorrhizal fungal community is pertinent to understand arbuscular mycorrhizal fungi and their crop hosts’ responses to anthropogenic influences.

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Stakeholder Involvement in Developing Environmental Indicators for the Lam Nam Yang Part 1 Watershed in the Northeastern Thailand

Applied Environmental Research ◽

10.35762/aer.2018.40.3.4 ◽

2018 ◽

pp. 28-41

Author(s):

Warintorn Khunanake ◽

Art-ong Pradatsudara ◽

Sura Pattanakiat

Keyword(s):

Watershed Management ◽

Stakeholder Involvement ◽

Environmental Issues ◽

Water Shortage ◽

Environmental Indicators ◽

Dpsir Framework ◽

Key Informant ◽

Management Plans ◽

Biodiversity Decline

Stakeholder involvement is recognized as critical to successful long-term watershed management.Approaches to developing sustainable watershed management plans are based upon selection and weighting of a set of relevant indicators on which the watershed’s sustainability and health can be measured. This study aimed to identify key environmental issues affecting the Lam Nam Yang Part 1 watershed in Thailand, and to work with stakeholders to develop a set of environmental indicators to support sustainable watershed management. The study used a community survey and key informant interviews to obtain stakeholder inputs into the process. Applying the Driver-Pressure-State-Impact-Response (DPSIR) framework, key environmental issues were identified and used to frame environmental indicators for the Lam Nam Yang Part 1 watershed. Key environmental issues identified included drought and water shortage, forest area depletion, biodiversity decline, and soil deterioration. A total of 101 candidate indicators were identified for monitoring the sustainability of the Lam Nam Yang Part 1 watershed, with 31 prioritized.

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Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system

PeerJ ◽

10.7717/peerj.7762 ◽

2019 ◽

Vol 7 ◽

pp. e7762 ◽

Cited By ~ 2

Author(s):

Hai-Sheng Dong ◽

Pu Chen ◽

Yan-Bo Yu ◽

Peng Zang ◽

Zhao Wei

Keyword(s):

Support System ◽

Gut Microbiome ◽

Large Scale ◽

Life Support ◽

Alpha Diversity ◽

Life Support System ◽

Fecal Microbiome ◽

Hydroxyvitamin D ◽

25 Hydroxyvitamin D

Background Changes in gut microbiome are closely related to dietary and environment variations, and diurnal circle interventions impact on human metabolism and the microbiome. Changes in human gut microbiome and serum biochemical parameters during long-term isolation in a controlled ecological life support system (CELSS) are of great significance for maintaining the health of crewmembers. The Green Star 180 project performed an integrated study involving a four-person, 180-day duration assessment in a CELSS, during which variations in gut microbiome and the concentration of serum 25-hydroxyvitamin D, α-tocopherol, retinol and folic acid from the crewmembers were determined. Results Energy intake and body mass index decreased during the experiment. A trade-off between Firmicutes and Bacteroidetes during the study period was observed. Dynamic variations in the two dominant genus Bacteroides and Prevotella indicated a variation of enterotypes. Both the evenness and richness of the fecal microbiome decreased during the isolation in the CELSS. Transition of diurnal circle from Earth to Mars increased the abundance of Fusobacteria phylum and decreased alpha diversity of the fecal microbiome. The levels of serum 25-hydroxyvitamin D in the CELSS were significantly lower than those outside the CELSS. Conclusions The unique isolation process in the CELSS led to a loss of alpha diversity and a transition of enterotypes between Bacteroides and Prevotella. Attention should therefore be paid to the transition of the diurnal circle and its effects on the gut microbiome during manned Mars explorations. In particular, serum 25-hydroxyvitamin D levels require monitoring under artificial light environments and during long-term space flight. Large-scale studies are required to further consolidate our findings.

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Effects of Long-term Cotton Continuous Cropping on Soil Microbiome

Scientific Reports ◽

10.1038/s41598-019-54771-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Hui Xi ◽

Jili Shen ◽

Zheng Qu ◽

Dingyi Yang ◽

Shiming Liu ◽

...

Keyword(s):

Severe Disease ◽

Soil Microbial Communities ◽

Alpha Diversity ◽

Taxonomic Composition ◽

Soil Microbiome ◽

Continuous Cropping ◽

Bacterial Phyla ◽

Soil Microbial ◽

Microbial Groups

AbstractVerticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

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Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome

Microorganisms ◽

10.3390/microorganisms8020179 ◽

2020 ◽

Vol 8 (2) ◽

pp. 179

Author(s):

Wendy S.W. Wong ◽

Priya Sabu ◽

Varsha Deopujari ◽

Shira Levy ◽

Ankit A. Shah ◽

...

Keyword(s):

Cesarean Section ◽

Vaginal Delivery ◽

Alpha Diversity ◽

Antibiotic Use ◽

Birth Cohort Study ◽

Delivery Mode ◽

Differential Abundance ◽

Bacterial Dna ◽

Cesarean Section Delivery

The meconium microbiome may provide insight into intrauterine and peripartum exposures and the very earliest intestinal pioneering microbes. Prenatal antibiotics have been associated with later obesity in children, which is thought to be driven by microbiome dependent mechanisms. However, there is little data regarding associations of prenatal or peripartum antibiotic exposure, with or without cesarean section (CS), with the features of the meconium microbiome. In this study, 16S ribosomal RNA gene sequencing was performed on bacterial DNA of meconium samples from 105 infants in a birth cohort study. After multivariable adjustment, delivery mode (p = 0.044), prenatal antibiotic use (p = 0.005) and peripartum antibiotic use (p < 0.001) were associated with beta diversity of the infant meconium microbiome. CS (vs. vaginal delivery) and peripartum antibiotics were also associated with greater alpha diversity of the meconium microbiome (Shannon and Simpson, p < 0.05). Meconium from infants born by CS (vs. vaginal delivery) had lower relative abundance of the genus Escherichia (p < 0.001). Prenatal antibiotic use and peripartum antibiotic use (both in the overall analytic sample and when restricting to vaginally delivered infants) were associated with differential abundance of several bacterial taxa in the meconium. Bacterial taxa in the meconium microbiome were also differentially associated with infant excess weight at 12 months of age, however, sample size was limited for this comparison. In conclusion, prenatal and peripartum antibiotic use along with CS delivery were associated with differences in the diversity and composition of the meconium microbiome. Whether or not these differences in the meconium microbiome portend risk for long-term health outcomes warrants further exploration.

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Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study

PeerJ ◽

10.7717/peerj.4693 ◽

2018 ◽

Vol 6 ◽

pp. e4693 ◽

Cited By ~ 24

Author(s):

Christopher J. Stewart ◽

Thomas A. Auchtung ◽

Nadim J. Ajami ◽

Kenia Velasquez ◽

Daniel P. Smith ◽

...

Keyword(s):

Pilot Study ◽

Gut Microbiota ◽

Tobacco Smoking ◽

Electronic Cigarettes ◽

Alpha Diversity ◽

Rrna Gene ◽

Cross Sectional ◽

Buccal Swabs ◽

Significant Difference

BackgroundThe use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls.MethodsWe examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing.ResultsTobacco smoking had a significant effect on the bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with an increased relative abundance ofPrevotella(P= 0.006) and decreasedBacteroides(P= 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced (P= 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls.DiscussionFrom a microbial ecology perspective, the current pilot data demonstrate that the use of ECs may represent a safer alternative compared to tobacco smoking. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted.

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Effect of Calcium Cyanamide on Soil Fungal Community in Successive Tea-Cuttings Nursery

Agriculture ◽

10.3390/agriculture11080716 ◽

2021 ◽

Vol 11 (8) ◽

pp. 716

Author(s):

Qinli Qiu ◽

Dongmei Fan ◽

Yinmao Wang ◽

Danyi Huang ◽

Yu Wang ◽

...

Keyword(s):

Plant Pathogens ◽

High Throughput Sequencing ◽

Aluminum Toxicity ◽

Ph Value ◽

Alpha Diversity ◽

Pathogenic Fungi ◽

Available Phosphorus ◽

Calcium Cyanamide ◽

Exchangeable Al

The effects of calcium cyanamide on the soil fungal communities in successive tea-cuttings nursery soils were investigated based on Illumina high-throughput sequencing. The field experiment was carried out with three treatments, including control (CK), flooding (F) and calcium cyanamide (CC). The treatment with calcium cyanamide increased pH (~1 unit) and reduced the accumulation of phenols (~50%), available phosphorus (~28%) and exchangeable Al (~90%) significantly, and improved soil quality. The predominant phylum in all treatments was Ascomycota. FUNGuild revealed that the dominant trophic mode was saprotrophy in tea-cuttings nursery soil. Plant pathogens had a low abundance in the calcium cyanamide treatment. Alpha diversity analysis showed lower richness in the calcium cyanamide than the other treatments. Network analysis showed a poorly connected but highly modularized network in the calcium cyanamide treatment, with the crucial OTUs functions related to anti-pathogenicity. The results showed that calcium cyanamide should be recommended for improving long-term tea nurseries by increasing the survival rate of tea seedlings due to increasing soil pH value, reducing aluminum toxicity, decreasing the accumulation of polyphenols, diminishing pathogenic fungi and making the taxa related to anti-pathogenicity occupy a more important niche.

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