Does functional soil microbial diversity contribute to explain within-site plant beta-diversity in an alpine grassland and a <i>dehesa</i> meadow in Spain?

Questions: Once that the effects of hydrological and chemical soil properties have been accounted for, does soil microbial diversity contribute to explain change in plant community structure (i.e. within-site beta-diversity)? If so, at which spatial scale does microbial diversity operate? Location: La Mina in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga in the Urbión Peaks, Soria, central-northern Spain (alpine grassland). Methods: The abundance of vascular plant species, soil gram-negative microbial functional types and soil chemical properties (pH, available phosphorus, and extractable cations) were sampled at both sites, for which hydrological models were available. Redundancy analysis (RDA) was used to partition variation in plant community structure into hydrological, chemical and microbial components. Spatial filters, arranged in scalograms, were used to test for the spatial scales at which plant community structure change. Results: In the case of the dehesa the diversity of soil gram-negative microbes, weakly driven by soil pH, contributed to a small extent (adj-R2 = 2%) and at a relative medium spatial scale to explain change in plant community structure. The abundance of a few dehesa species, both annual (Trifolium dubium, Vulpia bromoides) and perennial (Poa bulbosa, Festuca ampla), was associated with either increasing or decreasing soil microbial diversity. In the alpine meadow the contribution was negligible. Conclusions: Microbial diversity can drive community structure, though in the hierarchy of environmental factors structuring communities it appears to rank lower than other soil factors. Still, microbial diversity appears to promote or restrain individual plant species. This paper aims to encourage future studies to use more comprehensive and insightful techniques to assess microbial diversity and to combine this with statistical approaches such as the one used here

Editorial: Microbial Taxonomy, Phylogeny and Biodiversity

The great diversity of microbial life is the remaining majorreservoir of unknown biologicaldiversity on Earth. To understand this vast, but largely unperceived diversity with its untappedgenetic, enzymatic and industrial potential, microbial systematics is undergoing a revolutionarychange in its approach to describe novel taxa based on genomic/envirogenomic information(Rosselló-Móra and Whitman, 2019)S

Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities.

A remaining challenge within microbial ecology is to understand the determinants of richness and diversity observed in environmental microbial communities. In a range of systems, including activated sludge bioreactors, the microbial residence time (MRT) has been previously shown to shape the microbial community composition. However, the physiological and ecological mechanisms driving this influence have remained unclear. Here, this relationship is explored by analyzing an activated sludge system fed with municipal wastewater. Using a model designed in this study based on Monod-growth kinetics, longer MRTs were shown to increase the range of growth parameters that enable persistence, resulting in increased richness and diversity in the modeled community. In laboratory experiments, six sequencing batch reactors treating domestic wastewater were operated in parallel at MRTs between 1 and 15 days. The communities were characterized using both 16S ribosomal RNA and non-target messenger RNA sequencing (metatranscriptomic analysis), and model-predicted monotonic increases in richness were confirmed in both profiles. Accordingly, taxonomic Shannon diversity also increased with MRT. In contrast, the diversity in enzyme class annotations resulting from the metatranscriptomic analysis displayed a non-monotonic trend over the MRT gradient. Disproportionately high abundances of transcripts encoding for rarer enzymes occur at longer MRTs and lead to the disconnect between taxonomic and functional diversity profiles

Microbial diversity in Baltic Sea sediments

This thesis focuses on microbial community structures and their functions in Baltic Sea sediments. First we investigated the distribution of archaea and bacteria in Baltic Sea sediments along a eutrophication gradient. Community profile analysis of 16S rRNA genes using terminal restriction length polymorphism (T-RFLP) indicated that archaeal and bacterial communities were spatially heterogeneous. By employing statistical ordination methods we observed that archaea and bacteria were structured and impacted differently by environmental parameters that were significantly linked to eutrophication. In a separate study, we analyzed bacterial communities at a different site in the Baltic Sea that was heavily contaminated with polyaromatic hydrocarbons (PAHs) and several other pollutants. Sediment samples were collected before and after remediation by dredging in two consecutive years. A polyphasic experimental approach was used to assess growing bacteria and degradation genes in the sediments. The bacterial communities were significantly different before and after dredging of the sediment. Several isolates collected from contaminated sediments showed an intrinsic capacity for degradation of phenanthrene (a PAH model compound). Quantititative real-time PCR was used to monitor the abundance of degradation genes in sediment microcosms spiked with phenanthrene. Although both xylE and phnAc genes increased in abundance in the microcosms, the isolates only carried phnAc genes. Isolates with closest 16S rRNA gene sequence matches to Exigobacterium oxidotolerans, a Pseudomonas sp. and a Gammaproteobacterium were identified by all approaches used as growing bacteria that are capable of phenanthrene degradation. These isolates were assigned species and strain designations as follows: Exiguobacterium oxidotolerans AE3, Pseudomonas fluorescens AE1 and Pseudomonas migulae AE2. We also identified and studied the distribution of actively growing bacteria along red-ox profiles in Baltic Sea sediments. Community structures were found to be significantly different at different red-ox depths. Also, according to multivariate statistical ordination analysis organic carbon, nitrogen, and red-ox potential were crucial parameters for structuring the bacterial communities on a vertical scale. Novel lineages of bacteria were obtained by sequencing 16S rRNA genes from different red-ox depths and sampling stations indicating that bacterial diversity in Baltic Sea sediments is largely unexplored

Microbial and metabolic succession on common building materials under high humidity conditions.

Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material

Diversity and biosynthetic potential of culturable microbes associated with toxic marine animals

Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus

Phyllosphere microbiology with special reference to diversity and plant genotype

The phyllosphere represents the habitat provided by the aboveground parts of plants, and on a global scale supports a large and complex microbial community. Microbial interactions in the phyllosphere can affect the fitness of plants in natural communities, the productivity of agricultural crops, and the safety of horticultural produce for human consumption. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonists, which is influenced by numerous environmental factors in addition to leaf physico-chemical properties. The recent use of culture-independent techniques has demonstrated considerable previously unrecognized diversity in phyllosphere bacterial communities. Furthermore, there is significant recent evidence that plant genotype can play a major role in determining the structure of phyllosphere microbial communities. The main aims of this review are: (i) to discuss the diversity of phyllosphere microbial populations; (ii) to consider the processes by which microbes colonize the phyllosphere; (iii) to address the leaf characteristics and environmental factors that determine the survival and growth of colonists; (iv) to discuss microbial adaptations that allow establishment in the phyllosphere habitat and (v) to evaluate evidence for plant genotypic control of phyllosphere communities. Finally, we suggest approaches and priority areas for future research on phyllosphere microbiology