Franziska Wemheuer's research while affiliated with Georg-August-Universität Göttingen and other places
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Publications (81)
Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the acti...
Coastal systems such as estuaries are threatened by multiple anthropogenic stressors worldwide. However, how these stressors and estuarine hydrology shape benthic bacterial communities and their functions remains poorly known. Here, we surveyed sediment bacterial communities in poorly flushed embayments and well flushed channels in Sydney Harbour,...
Intercropping of legumes and cereals provides many ecological advantages and contributes to a sustainable agriculture. These agricultural systems face ongoing shifts in precipitation patterns and seasonal drought. Although the effect of drought stress on legumes has been frequently studied, knowledge about water deficits influencing legumes under d...
Widespread wastewater pollution is one of the greatest challenges threatening the sustainable management of rivers globally. Understanding microbial responses to gradients in environmental stressors, such as wastewater pollution, is crucial to identify thresholds of community change and to develop management strategies that protect ecosystem integr...
Real-world observational datasets that record and quantify pressure-stressor-response linkages between effluent discharges and natural aquatic systems are rare. With global wastewater volumes increasing at unprecedented rates, it is urgent that the present dataset is available to provide the necessary information about microbial community structure...
Background:
Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology...
Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of T. cacao. To close this knowledge gap, we investigated the diversity, community compositi...
Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands...
Table S1: sampling site characteristics and alpha diversity values.
Table S2: sequence characteristics and accession numbers.
Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment sample...
Data S1: R code example for PERMANOVA analysis with rarefied OTU tables.
Table S4: functional predictions made with Tax4Fun2.
Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species...
Assessing the functional capability and redundancy of a microbial community is a major challenge in environmental microbiology. To address this challenge, we developed Tax4Fun2, a R-based tool for the rapid prediction of functional profiles and functional redundancy of prokaryotic communities from 16S rRNA gene sequences. By incorporating user-defi...
This report summarises those field campaigns, details the datasets
obtained and highlights the relevance of the data gathered to the overall modelling program for the Hunter River estuary water quality modelling project.
Ongoing intensification of rice production systems in Southeast Asia is causing devastating yield losses each year due to rice hoppers. Their continuing development of immunity to resistant rice varieties and pesticide applications further complicates this problem. Hence, there is a high demand for biological control agents of rice hoppers. Egg par...
Here, we report the 7.4-Mb draft genome sequence of Paenibacillus sp. strain GM2FR, an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Genome analysis revealed 6,652 coding gene sequences and several gene clusters involved in plant growth promotion, such as that for the siderophore bacillibactin.
Bacillus mycoides
GM6LP is an endophyte isolated from plant tissues ofLolium perenneL. Here, we report its draft genome sequence (6.2 Mb), which contains 96 contigs and 6,129 protein-coding genes. Knowledge about its genome will enable us to evaluate the potential use of GM6LP as a plant growth-promoting bacterium.
Bacillus mycoides GM5LP is a Gram-positive endophytic bacterium isolated from aerial plant tissues of Lolium perenne L. The 6.0-Mb draft genome harbors 6,132 protein-coding sequences, some of which might be involved in the biosynthesis of antimicrobial substances.
Paenibacillus amylolyticus strain GM1FR is an endophyte isolated from aerial plant tissues of Festuca rubra L. Here, we report the draft genome sequence (7.3 Mb) of GM1FR containing 6,241 protein-coding genes, some of which are potentially involved in plant growth promotion and biocontrol.
On-going intensification of rice production systems in Southeast Asia is causing devastating yield losses each year due to rice hoppers. Continuing development of immunity to resistant rice varieties and pesticide application further complicate this problem. Hence, there is a high demand for biological control agents. Egg parasitoid wasps are among...
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition al...
Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment...
Here, we report the draft genome sequence of Bacillus pumilus GM3FR, an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. The draft genome consists of 3.5 Mb and harbors 3,551 predicted protein-encoding genes. The genome provides insights into the biocontrol potential of B. pumilus GM3FR.
Pseudomonas putida GM4FR is an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Functional annotation of the draft genome (7.1 Mb) revealed 6,272 predicted protein-encoding genes. The genome provides insights into the biocontrol and plant growth-promoting potential of P. putida GM4FR.
Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass s...
Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active...
Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have great...
Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils de...
Unlabelled:
Most plant species are colonized by endophytic bacteria. Despite their importance for plant health and growth, the response of these bacteria to grassland management regimes is still not understood. Hence, we investigated the bacterial community structure in three agricultural important grass species Dactylis glomerata L., Festuca rubr...
Verticillium wilt causes severe yield losses in a broad range of economically important crops worldwide. As many soil fumigants have a severe environmental impact, new biocontrol strategies are needed. Members of the genus Bacillus are known as plant growth-promoting bacteria as well as biocontrol agents of pests and diseases. In this study, we iso...
Redundancy analysis (RDA) of the functional bacterial community profiles derived from fertilizer and non-fertilizer treatments (A), and entire and active bacterial communities (B).
(PDF)
Chao1, Michaelis-Menten-Fit (MMF), observed OTUs, Shannon indices, Simpson indices and coverage at 20% genetic distance (phylum level) calculated for non-fertilized soil samples.
(PDF)
Rarefaction curves at 20% genetic distance calculated for the entire bacterial community in fertilized plots (fe_DNA:20%), active bacterial community in fertilized plots (fe_RNA:20%), entire bacterial community in non-fertilized plots (nf_DNA:20%), and active bacterial community in non-fertilized plots (nf_RNA:20%).
(PDF)
Climatic conditions in 2010 and 2011 at the sampling site.
(PDF)
Rarefaction curves at 3% genetic distance calculated for the entire bacterial community in fertilized plots (fe_DNA:3%), active bacterial community in fertilized plots (fe_RNA:3%), entire bacterial community in non-fertilized plots (nf_DNA:3%), and active bacterial community in non-fertilized plots (nf_RNA:3%).
(PDF)
Number of 16S rRNA gene sequences derived from the analyzed soil samples.
(PDF)
Chao1, Michaelis-Menten-Fit (MMF), observed OTUs, Shannon indices, Simpson indices and coverage at 20% genetic distance (phylum level) calculated for fertilized soil samples.
(PDF)
Chao1, Michaelis-Menten-Fit (MMF), observed OTUs, Shannon indices, Simpson indices and coverage at 3% genetic distance (species level) calculated for non-fertilized soil samples.
(PDF)
Chao1, Michaelis-Menten-Fit (MMF), observed OTUs, Shannon indices, Simpson indices and coverage at 3% genetic distance (species level) calculated for fertilized soil samples.
(PDF)
Boxplot diagram of the number of taxonomic units (OTUs) at 20% genetic distance over sampling time at DNA and RNA level.
1; April 2010, 2; July 2010, 3; September 2010, 4; April 2011, 5; July 2011, and 6; September 2011.
(PDF)
Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the respon...
Soil properties in fertilized and non-fertilized samples
(PDF)
Relative abundances of rare phyla (< 1% abundance) derived from the analyzed soil samples.
Fertilized (fe) and non-fertilized (nf) samples are shown in this figure. Samples were taken in April (Apr), July (Jul), and September (Sep) in 2010 (10) and 2011 (11) and the entire (D) and active (R) bacterial communities were analyzed.
(PDF)
Phytoplankton blooms exhibit a severe impact on bacterioplankton communities as they change nutrient availabilities and other environmental factors. In the current study, the response of a bacterioplankton community to a Phaeocystis globosa spring bloom was investigated in the southern North Sea. For this purpose, water samples were taken inside an...
In the last years, plant-associated bacterial communities caught the attention of investigators due to their importance for both plant health and the environmental balance. Despite the increasing number of studies, there is still a knowledge gap about the influence of management regimes on the diversity of plant-associated bacteria in grassland eco...
Volcanic regions contain a variety of environments suitable for extremophiles. This study was focused on assessing and exploiting the prokaryotic diversity of two microbial communities derived from different Kamchatkian thermal springs by metagenomic approaches. Samples were taken from a thermoacidophilic spring near the Mutnovsky Volcano and from...
Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these...
Citations
... The filter was kept at −80°C until further usage. The total community DNA was extracted according to Hollensteiner et al. (1). Illumina pair-end sequencing libraries were prepared and indexed using the Nextera DNA Flex library preparation kit and the Nextera DNA CD index kit as recommended by the manufacturer (Illumina, San Diego, CA, USA). ...
... Bracewell et al. (2023) identified similarities in benthic bacterial and eukaryotic communities across the upper catchments of temperate estuaries in eastern Australia, though bacteria appeared to be the most susceptible to immediate environmental changes. Previous research in highly urbanized estuaries like Sydney Harbour suggests that particularly species of bacteria may serve as useful indicators for localised anthropogenic stressors (Birrer et al., 2021). ...
... Because of the RWC limitation in drought-exposed plants, the main biochemical processes like photosynthesis may be restricted, which finally leads to declines in plant growth and development (Afshari et al. 2021). Similar to this work, the reduced RWC under drought stress has been addressed by Mehrasa et al. (2022), Bano et al. (2021), Meißner et al. (2021) on different bean spices. The foliar application of CS-NPs improved stomatal properties and water status in plants, which finally leads to increased photosynthesis rate and growth. ...
... All experiments were conducted under a 12 h light/12 h dark cycle and a constant temperature of 25° C 15,16 . After 2 days of water stabilization and clarification, aquatic animals (shrimp, snails, and fish) were placed in the simulation box for 45 days. ...
... However, single-species tests have limited ability to accurately predict direct and indirect effects on natural microbial populations, and very limited real-world relevance to ecosystemlevel impacts of environmental stressors ( Brandt et al., 2004 ;Guckert, 1996 ). The combination of community-level whole effluent toxicity (WET) testing and environmental genomics moves beyond the scenario of single species toxicity testing and provides the opportunity to determine real-world community interactions, shifts and functional change in response to wastewater pollution ( Ruprecht et al., 2020a ). ...
... Furthermore, most previous studies have solely conducted structural analyses without considering functional aspects, which cannot provide significant insights into the mechanism of gastric carcinogenesis. To elucidate the role of bacteria in the occurrence of GC, concurrent metagenomic functional analyses should yield more revealing results [7]. Therefore, we aimed to characterize the changes in the microbiome during gastric carcinogenesis and assess its predictable functional profiles. ...
... The challenge in investigating the aboveground-belowground interactions in an agroforestry system begins with the multiple components or subsystems that play a major role in determining system functioning. Research on Amazonian forests to date has generally focused on tree-crop interactions (González & Kröger, 2020;Maezumi et al., 2018;Pinho et al., 2011Pinho et al., , 2012Stabile et al., 2020) or plant-animal interactions, and few studies in other tropical regions (Africa, Central America, and Asia) considered the impact of agroforestry practices on soil microorganisms (Liu et al., 2019;Schneider et al., 2015;Wemheuer et al., 2020). To our knowledge, no studies have considered the interaction between above-and belowground in a holistic approach including soil microbiome, the main players in soil nutrient cycling, in AFS and compared these systems with the secondary succession and mature Amazonian rainforests. ...
... The taxonomic and functional composition of fungal communities in leaves can be affected by several biotic and abiotic stressors. For example, fungal pathogens and bacteria can cause the regreening of senescent leaf tissues in Acer, while reducing the overall fungal richness and altering leaf fungal communities [7]. In contrast, fungal endophyte communities are not correlated with pathogenic symptoms in Vanilla or Eucalyptus plants, respectively affected by pathogenic fungi and a wasp [8,9]. ...
... The taxonomic genus Aciduliprofundum was noted to have candidates for classification. The scholars Duya et al. (2020) and Wemheuer et al. (2019) during their studies identified the taxonomic family Nitrosopumilaceae being dominant, which was different during this study as members of the said family had species who were not fully classified. ...
... This suggests that AMF tends to be impacted by plant groups. According to Wemheuer et al. [53], endophytic bacteria also enhance nutrient availability and facilitate nitrogen fixation from the atmosphere, which promotes plant growth and health. ...