Atmospheric aerosol particles of biological origin are a very diverse group of biological materials and structures, including microorganisms, dispersal units, fragments and excretions of biological organisms. In recent years, the impact of biological aerosol particles on atmospheric processes has been studied with increasing intensity, and a wealth of new information and insights has been gained. This review outlines the current knowledge on major categories of primary biological aerosol particles (PBAP): bacteria and archaea, fungal spores and fragments, pollen, viruses, algae and cyanobacteria, biological crusts and lichens and others like plant or animal fragments and detritus. We give an overview of sampling methods and physical, chemical and biological techniques for PBAP analysis (cultivation, microscopy, DNA/RNA analysis, chemical tracers, optical and mass spectrometry, etc.). Moreover, we address and summarise the current understanding and open questions concerning the influence of PBAP on the atmosphere and climate, i.e. their optical properties and their ability to act as ice nuclei (IN) or cloud condensation nuclei (CCN). We suggest that the following research activities should be pursued in future studies of atmospheric biological aerosol particles: (1) develop efficient and reliable analytical techniques for the identification and quantification of PBAP; (2) apply advanced and standardised techniques to determine the abundance and diversity of PBAP and their seasonal variation at regional and global scales (atmospheric biogeography); (3) determine the emission rates, optical properties, IN and CCN activity of PBAP in field measurements and laboratory experiments; (4) use field and laboratory data to constrain numerical models of atmospheric transport, transformation and climate effects of PBAP. Keywords: primary biological atmospheric aerosol; climate; cloud condensation nuclei; biology; atmospheric ice nuclei (Published: 22 February 2012) Citation: Tellus B 2012, 64 , 15598, DOI: 10.3402/tellusb.v64i0.15598

https://www.tandfonline.com/doi/pdf/10.3402/tellusb.v64i0.15598

Primary biological aerosol particles in the atmosphere: a review

1. The real variable 2. Scalars and vectors 3. Tensors 4. Matrices 5. Multiple integrals 6. Potential theory 7. Operational methods 8. Physical applications of the operational method 9. Numerical methods 10. Calculus of variations 11. Functions of a complex variable 12. Contour integration and Bromwich's integral 13. Contour integration 14. Fourier's theorem 15. The factorial and related functions 16. Solution of linear differential equations of the second order 17. Asymptotic expansions 18. The equations of potential, waves and heat conduction 19. Waves in one dimension and waves with spherical symmetry 20. Conduction of heat in one and three dimensions 21. Bessel functions 22. Applications of Bessel functions 23. The confluent hypergeometric function 24. Legendre functions and associated functions 25. Elliptic functions Notes Appendix on notation Index.

Methods of Mathematical Physics. By Harold Jeffreys and Bertha Swirles Jeffreys. Pp. viii, 679. 63s. 1946. (Cambridge University Press)

Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.

https://tandfonline.com/doi/pdf/10.1080/1040841X.2016.1208146

Critical review on biofilm methods

http://dbkgroup.org/dave_files/ACA2015_ShotgunWedding.pdf

A tutorial review: Metabolomics and partial least squares-discriminant analysis--a marriage of convenience or a shotgun wedding.

Bioaerosols in the Earth system: Climate, health, and ecosystem interactions

Microorganisms, such as bacteria, which might be present as contamination inside an industrial food or pharmaceutical clean room process need to be identified on short time scales in order to minimize possible health hazards as well as production downtimes causing financial deficits. Here we describe the first results of single-particle micro-Raman measurements in combination with a classification method, the so-called support vector machine technique, allowing for a fast, reliable, and nondestructive online identification method for single bacteria.

Chemotaxonomic Identification of Single Bacteria by Micro-Raman Spectroscopy: Application to Clean-Room-Relevant Biological Contaminations

Rapid microbial detection and identification with a high grade of sensitivity and selectivity is a great and challenging issue in many fields, primarily in clinical diagnosis, pharmaceutical, or food processing technology. The tedious and time-consuming processes of current microbiological approaches call for faster ideally on-line identification techniques. The vibrational spectroscopic techniques IR absorption and Raman spectroscopy are noninvasive methods yielding molecular fingerprint information; thus, allowing for a fast and reliable analysis of complex biological systems such as bacterial or yeast cells. In this short review, we discuss recent vibrational spectroscopic advances in microbial identification of yeast and bacterial cells for bulk environment and single-cell analysis. IR absorption spectroscopy enables a bulk analysis whereas micro-Raman-spectroscopy with excitation in the near infrared or visible range has the potential for the analysis of single bacterial and yeast cells. The inherently weak Raman signal can be increased up to several orders of magnitude by applying Raman signal enhancement methods such as UV-resonance Raman spectroscopy with excitation in the deep UV region, surface enhanced Raman scattering, or tip-enhanced Raman scattering. © 2008 International Society for Advancement of Cytometry

https://onlinelibrary.wiley.com/doi/pdf/10.1002/cyto.a.20682

Vibrational spectroscopy--a powerful tool for the rapid identification of microbial cells at the single-cell level.

Microbial contamination is not only a medical problem, but also plays a large role in pharmaceutical clean room production and food processing technology. Therefore many techniques were developed to achieve differentiation and identification of microorganisms. Among these methods vibrational spectroscopic techniques (IR, Raman and SERS) are useful tools because of their rapidity and sensitivity. Recently we have shown that micro-Raman spectroscopy in combination with a support vector machine is an extremely capable approach for a fast and reliable, non-destructive online identification of single bacteria belonging to different genera. In order to simulate different environmental conditions we analyzed in this contribution different Staphylococcus strains with varying cultivation conditions in order to evaluate our method with a reliable dataset. First, micro-Raman spectra of the bulk material and single bacterial cells that were grown under the same conditions were recorded and used separately for a distinct chemotaxonomic classification of the strains. Furthermore Raman spectra were recorded from single bacterial cells that were cultured under various conditions to study the influence of cultivation on the discrimination ability. This dataset was analyzed both with a hierarchical cluster analysis (HCA) and a support vector machine (SVM).

Micro-Raman spectroscopic identification of bacterial cells of the genus Staphylococcus and dependence on their cultivation conditions

Eukaryotes (such as yeasts) and prokaryotes (such as bacteria) differ in size, molecular complexity, etc. By definition, eukaryotic cells store their DNA in a separate internal compartment, the so-called nucleus. Owing to this molecular compartmentalization, the identification of yeast cells by vibrational spectroscopy at a single-cell level is challenging. This contribution reports on first results of micro-Raman analysis together with a hierarchical cluster analysis allowing for an online identification method for yeast cells at a single-cell level. For the classification analysis, an average spectrum from 10 different measuring points within a single yeast cell was used to overcome the heterogeneity of the yeast cells. Copyright © 2005 John Wiley & Sons, Ltd.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/jrs.1312

Raman spectroscopic identification of single yeast cells

Bacterial meningitis is a relevant public health concern. Despite the availability of modern treatment strategies it is still a life-threatening disease that causes significant morbidity and mortality. Therefore, an initial treatment approach plays an important role. For in-time identification of specific bacterial pathogens of the cerebrospinal fluid (CSF) and emerged antimicrobial and adjunctive treatment, microbiological examination is of major importance. This contribution spotlights the potential of micro-Raman spectroscopy as a biomedical assay for direct analysis of bacteria in cerebrospinal fluid of patients with bacterial meningitis. The influence of miscellaneous artificial environments on several bacterial species present during bacterial meningitis was studied by means of Raman spectroscopy. The application of chemometric data interpretation via hierarchical cluster analysis (HCA) allows for the differentiation of in vitro cultured bacterial cells and can also be achieved on a single cell level. Moreover as proof of principle the investigation of a CSF sample obtained from a patient with meningococcal meningitis showed that the cerebrospinal fluid matrix does not mask the Raman spectrum of a bacterial cell notably since via chemometric analysis with HCA an identification of N. meningitidis cells from patients with bacterial meningitis could be achieved.

Michaela Harz

Papers

Chemotaxonomic Identification of Single Bacteria by Micro-Raman Spectroscopy: Application to Clean-Room-Relevant Biological Contaminations

Vibrational spectroscopy--a powerful tool for the rapid identification of microbial cells at the single-cell level.

Micro-Raman spectroscopic identification of bacterial cells of the genus Staphylococcus and dependence on their cultivation conditions

Raman spectroscopic identification of single yeast cells

Direct analysis of clinical relevant single bacterial cells from cerebrospinal fluid during bacterial meningitis by means of micro-Raman spectroscopy.