The current taxonomy of the order Xanthomonadales is highly problematic and no comprehensive phylogenomic studies have been completed that include the most divergent members within the order. In this work, we have completed a phylogenomic analysis of a wide range of genomes, five of which were sequenced for the first time for this work, representing the vast majority of the diversity within the order Xanthomonadales. Using comparative genomic techniques, we have identified a large number of conserved signature inserts/deletions (CSIs) that are specifically found in different groups of related organisms, at different taxonomic levels, within the order. Our phylogenetic analyses do not support a monophyletic grouping of the members of the order Xanthomonadales and no CSIs were identified which are uniquely shared by all sequenced species within this order. However, our work has identified 10 CSIs which are specific to all members of the family Xanthomonadaceae and an additional 10 and 11 CSIs that are specific to one of two phylogenetically well-defined clades within the family Xanthomonadaceae. On the basis of the identified CSIs and the results of phylogenomic analyses, we propose a new taxonomic framework for the order Xanthomonadales. In this proposal, the families Algiphilaceae and Solimonadaceae (Nevskiaceae), which do not branch with the other members of the order Xanthomonadales, are transferred into the order Nevskiales ord. nov. The remaining members of the order Xanthomonadales are divided into two families: the family Xanthomonadaceae, containing the genus Xanthomonas and its closest relatives, and a new family, Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Additionally, we have also emended descriptions of the order Lysobacterales, the family Lysobacteraceae, and the family Nevskiaceae to indicate that they are earlier synonyms of the order Xanthomonadales, the family Xanthomonadaceae, and the family Solimonadaceae, respectively.
Phytoplankton monitoring is essential for better understanding and mitigation of phytoplankton bloom formation. We present a microfluidic cytometer with two imaging modalities for onsite detection and identification of phytoplankton: a lensless imaging mode for morphological features, and a fluorescence imaging mode for autofluorescence signal of phytoplankton. Both imaging modes are integrated in a microfluidic device with a field of view (FoV) of 3.7 mm × 2.4 mm and a depth of field (DoF) of 0.8 mm. The particles in the water flow channel can be detected and classified with automated image processing algorithms and machine learning models using their morphology and fluorescence features. The performance of the device was demonstrated by measuring Chlamydomonas, Euglena, and non-fluorescent beads in both separate and mixed flow samples. The recall rates for Chlamydomonas and Euglena ware 93.6% and 94.4%. The dual-modality imaging approach enabled observing both morphology and fluorescence features with a large DoF and FoV which contribute to high-throughput analysis. Moreover, this imaging flow cytometer platform is portable, low-cost, and shows potential in the onsite phytoplankton monitoring.
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