ORCID Profile
0000-0001-9253-4517
Current Organisation
Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Cold Spring Harbor Laboratory
Date: 11-12-2022
DOI: 10.1101/2022.12.07.518693
Abstract: Above Ground Biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically ≥1 ha) using inventory measurements and allometry. In recent years, Terrestrial Laser Scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of in idual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. Here we present TLS2trees , an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2trees consists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated across 10 plots of 7 forest types from open savanna to dense tropical rainforest, where a total of 10,557 trees are segmented. TLS2trees segmented trees are compared to 1,281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m 3 and %RMSE is ~ 60%. To facilitate improvements to the presented methods as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software (FOSS).
Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.SCITOTENV.2019.03.278
Abstract: Recycled wastewater can carry human-infectious microbial pathogens and therefore wastewater treatment strategies must effectively eliminate pathogens before recycled wastewater is used to supplement drinking and agricultural water supplies. This study characterised the bacterial composition of four wastewater treatment plants (WWTPs) (three waste stabilisation ponds and one oxidation ditch WWTP using activated sludge treatment) in Western Australia. The hypervariable region 4 (V4) of the bacterial 16S rRNA (16S) gene was sequenced using next-generation sequencing (NGS) on the Illumina MiSeq platform. Sequences were pre-processed in USEARCH v10.0 and denoised into zero-radius taxonomic units (ZOTUs) with UNOISE3. Taxonomy was assigned to the ZOTUs using QIIME 2 and the Greengenes database and cross-checked with the NCBI nr/nt database. Bacterial composition of all WWTPs and treatment stages (influent, intermediate and effluent) were dominated by Proteobacteria (29.0-87.4%), particularly Betaproteobacteria (9.0-53.5%) and Gammaproteobacteria (8.6-34.6%). Nitrifying bacteria (Nitrospira spp.) were found only in the intermediate and effluent of the oxidation ditch WWTP, and denitrifying and floc-forming bacteria were detected in all WWTPs, particularly from the families Comamonadaceae and Rhodocyclales. Twelve pathogens were assigned taxonomy by the Greengenes database, but comparison of sequences from genera and families known to contain pathogens to the NCBI nr/nt database showed that only three pathogens (Arcobacter venerupis, Laribacter hongkongensis and Neisseria canis) could be identified in the dataset at the V4 region. Importantly, Enterobacteriaceae genera could not be differentiated. Family level taxa assigned by Greengenes database agreed with NCBI nr/nt in most cases, however, BLAST analyses revealed erroneous taxa in Greengenes database. This study highlights the importance of validating taxonomy of NGS sequences with databases such as NCBI nr/nt, and recommends including the V3 region of 16S in future short licon NGS studies that aim to identify bacterial enteric pathogens, as this will improve taxonomic resolution of most, but not all, Enterobacteriaceae species.
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 05-2017
Publisher: Wiley
Date: 14-04-2023
DOI: 10.1002/RSE2.333
Abstract: Climate change and increasing human activities are impacting ecosystems and their bio ersity. Quantitative measurements of essential bio ersity variables (EBV) and essential climate variables are used to monitor bio ersity and carbon dynamics and evaluate policy and management interventions. Ecosystem structure is at the core of EBVs and carbon stock estimation and can help to inform assessments of species and species ersity. Ecosystem structure is also used as an indirect indicator of habitat quality and expected species richness or species community composition. Spaceborne measurements can provide large‐scale insight into monitoring the structural dynamics of ecosystems, but they generally lack consistent, robust, timely and detailed information regarding their full three‐dimensional vegetation structure at local scales. Here we demonstrate the potential of high‐frequency ground‐based laser scanning to systematically monitor structural changes in vegetation. We present a proof‐of‐concept high‐temporal ecosystem structure time series of 5 years in a temperate forest using terrestrial laser scanning (TLS). We also present data from automated high‐temporal laser scanning that can allow upscaling of vegetation structure scanning, overcoming the limitations of a typically opportunistic TLS measurement approach. Automated monitoring will be a critical component to build a network of field monitoring sites that can provide the required calibration data for satellite missions to effectively monitor the structural dynamics of vegetation over large areas. Within this perspective, we reflect on how this network could be designed and discuss implementation pathways.
Publisher: Elsevier BV
Date: 10-2022
Publisher: Copernicus GmbH
Date: 28-04-2016
Abstract: Abstract. The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is 2000 mm yr−1 (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall 2000 mm yr−1.
Publisher: American Chemical Society (ACS)
Date: 12-04-2017
Abstract: Chlorination of amino acids can result in the formation of organic monochloramines or organic dichloramines, depending on the chlorine to amino acid ratio (Cl:AA). After formation, organic chloramines degrade into aldehydes, nitriles and N-chloraldimines. In this paper, the formation of organic chloramines from chlorination of lysine, tyrosine and valine were investigated. Chlorination of tyrosine and lysine demonstrated that the presence of a reactive secondary group can increase the Cl:AA ratio required for the formation of N,N-dichloramines, and potentially alter the reaction pathways between chlorine and amino acids, resulting in the formation of unexpected byproducts. In a detailed investigation, we report rate constants for all reactions in the chlorination of valine, for the first time, using experimental results and modeling. At Cl:AA = 2.8, the chlorine was found to first react quickly with valine (5.4 × 10
Publisher: Wiley
Date: 21-10-2023
Location: Germany
Location: Germany
No related grants have been discovered for Benjamin Brede.