Article
Environmental Sciences
Yuan Xu, Janne Soininen, Shukun Zhang, Xinpeng Fan
Summary: The study revealed that in a highly disturbed estuarine bay in China, the diversity of benthic ciliates is influenced by environmental gradients, with sediment grain size and heavy metals being the key determining factors. Human induced nitrogen enrichment may have impacts on benthic food webs.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Chidanandamurthy Thippeswamy Swamy, Devaraja Gayathri
Summary: This study utilized next generation sequencing to investigate bacterial diversity in foliose lichens, revealing significant microbial variations between different lichens and diverse relative abundances of dominant and rare bacterial species. The predominant bacterial phyla found in all tested lichens were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Biodiversity Conservation
Ning Zong, Gang Fu
Summary: Desertification can impact global socioeconomic development, ecological safety, and human health. In a field experiment in the Northern Tibet, it was found that species diversity and function diversity were affected by desertification, with soil fungal communities playing a key role in element cycling. Monitoring desertification conditions may be improved by combining species and function composition.
ECOLOGICAL INDICATORS
(2021)
Article
Multidisciplinary Sciences
Samantha L. Rumschlag, Michael B. Mahon, Devin K. Jones, William Battaglin, Jonny Behrens, Emily S. Bernhardt, Paul Bradley, Ethan Brown, Frederik De Laender, Ryan Hill, Stefan Kunz, Sylvia Lee, Emma Rosi, Ralf Schaefer, Travis S. Schmidt, Marie Simonin, Kelly Smalling, Kristofor Voss, Jason R. Rohr
Summary: Based on the analysis of 6131 stream sites across different land uses in the United States over a period of 27 years, it was found that macroinvertebrate density declined by 11% and richness increased by 12.2%. Insect density and richness showed even greater declines of 23.3% and 6.8%, respectively. Furthermore, there was an increasing difference in richness and composition between urban and agricultural streams compared to forested and grassland streams. Urban and agricultural streams lost disturbance-sensitive taxa and gained disturbance-tolerant taxa. These findings indicate that current stream protection and restoration efforts are insufficient to mitigate the impacts of human activities.
Article
Plant Sciences
La-Mei Jiang, Kunduz Sattar, Guang-Hui Lu, Dong Hu, Jie Zhang, Xiao-Dong Yang
Summary: This study compared changes in community stability and different plant diversity across different spatial scales and communities, and quantified the contribution of soil properties and plant diversity to community stability. The results showed that plant diversities had a greater effect on community stability than soil factors, with different communities exhibiting varying levels of stability across spatial scales.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Engineering, Environmental
Weiyu Li, Dan Luo, Ning Yan, Lingzhan Miao, Tanveer M. Adyel, Ming Kong, Jun Hou
Summary: This study investigated the effects of polyethylene microplastics (PE MPs) with different sizes and concentrations on biofilm communities. The results showed that the presence of MPs significantly altered the diversity and structure of the biofilm community and affected microbial-mediated processes.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2023)
Article
Agronomy
Nan Mei, Xiuzhi Zhang, Xinqi Wang, Chang Peng, Hongjun Gao, Ping Zhu, Yan Gu
Summary: Long-term fertilization significantly impacts soil bacterial communities, with different fertilization methods affecting bacterial diversity and soil properties differently. The use of organic fertilizers can significantly increase maize yield and soil nutrients, as well as enhance bacterial community diversity.
EUROPEAN JOURNAL OF AGRONOMY
(2021)
Article
Ecology
Anne Chao, Simon Thorn, Chun-Huo Chiu, Faye Moyes, Kai-Hsiang Hu, Robin L. Chazdon, Jessie Wu, Luiz Fernando S. Magnago, Maria Dornelas, David Zeleny, Robert K. Colwell, Anne E. Magurran
Summary: In this study, we propose a rigorous standardization method to measure and compare beta diversity across datasets based on sampling data. Our approach is built upon the assumption of a statistical sampling model, treating the sampling data as a representative sample from an assemblage. We introduce the concept of standardized, coverage-based beta diversity by standardizing alpha and gamma diversity at the same level of sample coverage. Our extension of the iNEXT method to beta diversity ensures the removal of the dependence on gamma and alpha values, allowing us to quantify the pure among-assemblage differentiation. The proposed standardization is demonstrated with various spatial, temporal, and spatiotemporal datasets.
ECOLOGICAL MONOGRAPHS
(2023)
Article
Biodiversity Conservation
Mateus M. Pires, Marta G. Grech, Cristina Stenert, Leonardo Maltchik, Luis B. Epele, Kyle I. McLean, Jamie M. Kneitel, Douglas A. Bell, Hamish S. Greig, Chase R. Gagne, Darold P. Batzer
Summary: The study found that family-level resolution can be used as a surrogate of finer taxonomic resolutions to describe invertebrate community structure patterns in New World freshwater wetlands without significant information loss. However, conclusions on biodiversity patterns derived from datasets with different numerical resolutions should be critically considered.
ECOLOGICAL INDICATORS
(2021)
Article
Ecology
Maede Faghihinia, Yi Zou, Yongfei Bai, Martin Dudas, Rob Marrs, Philip L. Staddon
Summary: The diversity and community composition of AMF in roots and rhizosphere soil of dominant perennial grasses were found to change in response to grazing intensity. Different virtual taxa of AMF showed varying responses along the grazing gradient, with Glomeraceae being the most abundant family. Grazing preference by sheep did not explain much of the variation in AMF diversity, but the two grass species exhibited different AMF community composition in their roots and rhizosphere soils. Overall, long-term grazing intensity may have favored disturbance-tolerant AMF taxa.
Article
Biodiversity Conservation
C. E. Simpkins, S. Hanss, M. C. Spangenberg, J. Salecker, M. H. K. Hesselbarth, K. Wiegand
Summary: Understanding the spatial distribution of biodiversity is crucial for ecology and conservation. We have developed a software package called spectre that can predict community composition at a fine spatial resolution using sparse biological data. The package uses a min-conflicts optimization algorithm to predict species' presences and absences in an area. It provides a simple and accurate tool for predicting community compositions across varying scales, facilitating further research and knowledge acquisition in ecology.
Article
Microbiology
Jie Kong, Lei Wang, Cai Lin, Fangfang Kuang, Xiwu Zhou, Edward A. Laws, Ping Sun, Hao Huang, Bangqin Huang
Summary: Bacteria and microeukaryotes play important roles in global biogeochemical cycles. In this study, the distribution patterns and assembly mechanisms of these microorganisms in the tropical North Pacific Ocean were investigated. The results showed significant biogeographic patterns and diversity differences between regions for both bacteria and microeukaryotes. The correlations between spatial and environmental variables and the alpha and beta diversities of these microorganisms were similar. Ecological drift was the main mechanism driving the bacterial communities, while heterogeneous selection, dispersal limitation, and ecological drift collectively explained the turnover of microeukaryote communities.
MICROBIOLOGY SPECTRUM
(2022)
Article
Geography, Physical
S. Karachurina, N. Rudaya, L. Frolova, O. Kuzmina, X. Cao, V. Chepinoga, K. Stoof-Leichsenring, B. Biskaborn, U. Herzschuh, N. Nigmatullin, Y. Vnukovskaya, I. Grekov, L. Pestryakova
Summary: Using pollen analysis and metabarcoding of plant sedaDNA, the study reveals the floristic diversity and dominant tree species in the vicinity of Lake Balyktukel, Altai Mountains, over the past 7,000 years. The sedaDNA method identified significantly more taxa compared to traditional pollen analysis, highlighting the dominance of Larix over Pinus. The study also reconstructs past climate conditions and indicates a correlation between maximum phytodiversity and humid phases.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2023)
Article
Engineering, Environmental
Mengdie Geng, Weizhen Zhang, Ting Hu, Rong Wang, Xiaoying Cheng, Jianjun Wang
Summary: This study investigated the effects of eutrophication on microbial community structure in shallow lakes in the Yangtze-Huaihe River basin in China. The results showed that eutrophication led to the homogenization of bacterial and fungal communities in both water and sediments. Physicochemical factors such as water temperature, pH, and heavy metals were found to influence the community structure. Importantly, generalist species were found to play a dominant role in explaining the variations in beta diversity along the trophic gradient.
Article
Multidisciplinary Sciences
Wei Zhao, Liuyang Shi, Xingbiao Wang, Jingjing Wang, Song Xu, Lei Ma, Wanyu Zhu, Xiaoxia Zhang, Yifan Han, Zhiyong Huang
Summary: This study investigated the temporal and spatial effects on the planktonic prokaryotic community composition in the coastal region of the Bohai Sea using high-throughput sequencing. The results demonstrated that seasonal variations significantly influenced the alpha and beta diversity of prokaryotes, with environmental factors such as temperature, pH, and ammonia nitrogen driving the community assembly.
SCIENTIFIC REPORTS
(2022)
Article
Hematology
Arvind Dev, Ruth Asch, Edward Jachimowicz, Nicole Rainville, Ashley Johnson, Emily Greenfest-Allen, Don M. Wojchowski
EXPERIMENTAL HEMATOLOGY
(2017)
Article
Multidisciplinary Sciences
W. Bruce Saunders, Emily Greenfest-Allen, Peter D. Ward
Article
Anatomy & Morphology
Eileen D. Grogan, Richard Lund
Article
Hematology
Paul D. Kingsley, Emily Greenfest-Allen, Jenna M. Frame, Timothy P. Bushnell, Jeffrey Malik, Kathleen E. McGrath, Christian J. Stoeckert, James Palis
Article
Mathematical & Computational Biology
Emily Greenfest-Allen, Jeffrey Malik, James Palis, Christian J. Stoeckert
BMC SYSTEMS BIOLOGY
(2013)
Article
Paleontology
Kathryn E. Mickle, Richard Lund, Eileen D. Grogan
Article
Biodiversity Conservation
W. B. Saunders, Emily Greenfest-Allen, David M. Work, S. V. Nikolaeva
Article
Zoology
Eileen D. Grogan, Richard Lund
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2011)
Article
Cell Biology
Matthew A. Held, Emily Greenfest-Allen, Su Su, Christian J. Stoeckert, Matthew P. Stokes, Don M. Wojchowski
CELLULAR SIGNALLING
(2020)
Article
Hematology
Matthew A. Held, Emily Greenfest-Allen, Edward Jachimowicz, Christian J. Stoeckert, Matthew P. Stokes, Antony W. Wood, Don M. Wojchowski
EXPERIMENTAL HEMATOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Pavel P. Kuksa, Emily Greenfest-Allen, Jeffrey Cifello, Matei Ionita, Hui Wang, Heather Issen, Po-Liang Cheng, Wan-Ping Lee, Li-San Wang, Yuk Yee Leung
Summary: Non-coding genetic variants outside of protein-coding genome regions play a crucial role in genetic and epigenetic regulation. Understanding their roles has become increasingly significant as these variants often dominate the findings of genome-wide association studies. This review focuses on the latest approaches for annotating and prioritizing non-coding variants discovered in whole-genome sequencing analyses, covering scalable annotation tools, databases, functional genomic resources, and machine learning-based predictive models. The review also discusses future research directions to enhance our understanding of disease etiology through the effective functional analysis of WGS-identified variants.
HUMAN MOLECULAR GENETICS
(2022)
Article
Genetics & Heredity
Pavel P. Kuksa, Yuk Yee Leung, Prabhakaran Gangadharan, Zivadin Katanic, Lauren Kleidermacher, Alexandre Amlie-Wolf, Chien-Yueh Lee, Liming Qu, Emily Greenfest-Allen, Otto Valladares, Li-San Wang
Summary: Querying and summarizing large-scale functional genomic and annotation data collections is a crucial step in genetic analysis. However, the heterogeneity and breadth of data sources and formats make this process difficult. FILER is a framework that provides streamlined access to harmonized genomic datasets, a scalable querying interface, and the ability to analyze user's experimental data. This resource is highly scalable and facilitates reproducible research.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Meeting Abstract
Hematology
Paul D. Kingsley, Jenna M. Frame, Emily Greenfest-Allen, Jeffrey Malik, Kathleen E. McGrath, Laura M. Iafrati, Timothy P. Bushnell, Christian Stoeckert, James Palis
Article
Geography, Physical
Huyue Song, Shixue Hu, Michael Benton, Dayong Jiang
Summary: This article examines the end Permian to Middle Triassic interval, which witnessed a significant marine mass extinction and delayed recovery. The focus is on Triassic marine sediments in South China, providing unique documentation of the collapse and recovery of marine ecosystems. Several papers analyze different fossils and their ecological significance, while others study biostratigraphy, reconstruct paleoenvironments, and link records to volcanic eruptions.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Mohammad Firoze Quamar, Upasana Swaroop Banerji, Biswajeet Thakur, Ratan Kar
Summary: The Indian Summer Monsoon is a crucial component of the Asian Monsoon System, impacting rainfall, agricultural productivity, and socio-economic growth in India and nearby regions. The central monsoon zone in India is more responsive to strong monsoon phases than weak ones.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Maria Laura Balestrieri, Valerio Olivetti, David Chew, Luca Zurli, Massimiliano Zattin, Foteini Drakou, Gianluca Cornamusini, Matteo Perotti
Summary: This study presents a multidisciplinary provenance study on legacy cores drilled in the central Ross Sea, Antarctica, providing insights into the oscillation of ice flows and advance and retreat phases of the West Antarctic Ice Sheet.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
P. Depuydt, S. Toucanne, C. Barras, S. Le Houedec, M. Mojtahid
Summary: This study provides a comprehensive overview of the dynamics of the upper branch of the Atlantic Meridional Overturning Circulation (AMOC) in the mid-latitudes of the Northeast Atlantic. It focuses on the European Slope Current (ESC) and its glacial equivalent known as the Glacial Eastern Boundary Current (GEBC). The study reveals significant changes in flow strength and ventilation during the glacial and deglaciation periods, as well as a gradual weakening of the slope current during the Holocene.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Junhee Park, Holly J. Stein, Judith L. Hannah, Svetoslav V. Georgiev, Oyvind Hammer, Snorre Olaussen
Summary: This study reports new Re-Os ages for black shales from Svalbard and evaluates the paleoenvironment during organic-rich shale deposition. The study also proposes correlations of specific Late Jurassic ammonite zones between the Boreal and Tethyan realms.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Guocheng Dong, Weijian Zhou, Feng Xian, Yunchong Fu, Li Zhang, Ling Tang, Pengkai Ding
Summary: The cause of ice-age cycles is still not fully understood, and studying the timing and magnitude of mountain glaciations can provide valuable insights. This study presents new dating results from the Niqingqu Valley in the Tibetan Plateau, showing multiple glacial activities prior to the Penultimate Glacial Maximum. The findings suggest that low atmospheric CO2 content and reduced summer solar insolation/high summer-monsoon precipitation played a role in these glacial fluctuations.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Haoran Dong, Zhitong Chen, Yucheng Wang, Jie Chen, Zhiping Zhang, Zhongwei Shen, Xinwei Yan, Jianbao Liu
Summary: Through sediment records from Lake Nanyi in the lower Yangtze, we found that anthropogenic fire activity played a dominant role in the region, and the temporal pattern of fire activity was asynchronous from east to west. Archaeological evidence suggests an inverse relationship between agricultural and population levels and fire intensity during the mid-Holocene, with fire intensity being influenced by the diversity of landscape types associated with pre-historic subsistence patterns. Overall, changes in regional water-level delayed the transition from hunting-gathering to agriculture in the lower Yangtze region.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Giovanni Coletti, Giulia Bosio, Alberto Collareta, Or Mordecai Bialik, Eleonora Regattieri, Irene Cornacchia, Gianni Insacco, John Buckeridge
Summary: This paper argues that sessile barnacles are an excellent proxy for palaeoenvironmental reconstructions. The shells of barnacles consist of diagenetically stable low-magnesium calcite and record short-term variations. Analyses of several Western Mediterranean barnacle-rich deposits demonstrate the utility of barnacles as proxies for water depth, distance from the coastline, and hydrodynamic conditions. Moreover, the stable isotope ratios of barnacle shells can provide detailed palaeoenvironmental information.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Feng Wu, Xinong Xie, Wen Yan, Youhua Zhu, Beichen Chen, Jianuo Chen, Mo Zhou
Summary: This paper describes the Quaternary evolution of Meiji Atoll in the southern South China Sea. The findings show how variations in sea surface temperature, eustatic sea level, and tectonics have influenced the development of the atoll. These findings have broader implications for understanding the Quaternary evolution of similar tropical carbonate atolls in the region.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Ana Mateos, Ericson Hoelzchen, Jesus Rodriguez
Summary: The Epivillafranchian and the transition to the Galerian was a period of environmental fluctuations and faunal turnover. Hominins and giant hyenas could coexist during the Epivillafranchian, but the transition to the Galerian led to a disruption of the scavenging niche, coinciding with the extinction of P. brevirostris.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Tianyu Du, Wensheng Zhang, Bing Li, Linjing Liu, Yuecong Li, Yawen Ge, Shiyong Yu
Summary: This article presents sedimentary evidence for a dramatic channel displacement of the lower Yellow River about 3000-2600 years ago, and explains the impact of this displacement on the geomorphology and human migration.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Johann Mueller, Michael M. Joachimski, Oliver Lehnert, Peep Mannik, Yadong Sun
Summary: The Late Ordovician mass extinction occurred during an ice age, with maximum ice coverage and a substantial drop in global sea level. This led to the exposure or shallowing of shallow tropical shelf environments. The study suggests that the burial rate of nutrient phosphorus (P) on shelves was minimal during this glacial period, leading to excess bioavailable P entering the open ocean and stimulating phytoplankton production, which in turn lowered oxygen concentrations.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Marina Addante, Patrizia Maiorano, Giovanna Scopelliti, Angela Girone, Maria Marino, Samanta Trotta, Antonio Caruso
Summary: This study presents the first high-resolution results on planktonic foraminiferal stable oxygen isotopes and calcareous plankton assemblages, providing insights into the glacial-interglacial variability and North Atlantic climate variability. The research also reveals evidence of the first significant southward migration of the Subarctic Front in the mid-latitudes.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Bing-Cai Liu, Rui-Wen Zong, Kai Wang, Jiao Bai, Yi Wang, Hong-He Xu
Summary: Phytogeography plays a vital role in the evolution of plants. This paper describes a new species of a spore-bearing plant from the upper Silurian period in West Junggar, China. By analyzing global Silurian macrofossil records, the study reveals the spatial-temporal distribution of Silurian plant macrofossils and identifies two phytogeographic realms during the Pridoli Epoch.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)
Article
Geography, Physical
Francois Fournier, Thomas Teillet, Alexis Licht, Jean Borgomano, Lucien Montaggioni
Summary: This study investigates the temporal evolution of neritic carbonates in the proto-South China Sea to reconstruct East Asian monsoonal currents and winds during the middle to late Paleogene. The results highlight that many of the features of the summer East Asian Monsoon large-scale circulation are rooted in the middle Paleogene.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2024)