Invertebrate and Microbial Response to Hyporheic Restoration of an Urban Stream

All cities face complex challenges managing urban stormwater while also protecting urban water bodies. Green stormwater infrastructure and process-based restoration offer alternative strategies that prioritize watershed connectivity. We report on a new urban floodplain restoration technique being tested in the City of Seattle, USA: an engineered hyporheic zone. The hyporheic zone has long been an overlooked component in floodplain restoration. Yet this subsurface area offers enormous potential for stormwater amelioration and is a critical component of healthy streams. From 2014 to 2017, we measured hyporheic temperature, nutrients, and microbial and invertebrate communities at three paired stream reaches with and without hyporheic restoration. At two of the three pairs, water temperature was significantly lower at the restored reach, while dissolved organic carbon and microbial metabolism were higher. Hyporheic invertebrate density and taxa richness were significantly higher across all three restored reaches. These are some of the first quantified responses of hyporheic biological communities to restoration. Our results complement earlier reports of enhanced hydrologic and chemical functioning of the engineered hyporheic zone. Together, this research demonstrates that incorporation of hyporheic design elements in floodplain restoration can enhance temperature moderation, habitat diversity, contaminant filtration, and the biological health of urban streams.

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

Relevance and diversity of Nitrospira populations in biofilters of brackish RAS

Lithoautotrophic nitrite-oxidizing bacterial populations from moving-bed biofilters of brackish recirculation aquaculture systems (RAS; shrimp and barramundi) were tested for their metabolic activity and phylogenetic diversity. Samples from the biofilters were labeled with (13)C-bicarbonate and supplemented with nitrite at concentrations of 0.3, 3 and 10 mM, and incubated at 17 and 28°C, respectively. The biofilm material was analyzed by fatty acid methyl ester - stable isotope probing (FAME-SIP). High portions of up to 45% of Nitrospira-related labeled lipid markers were found confirming that Nitrospira is the major autotrophic nitrite oxidizer in these brackish systems with high nitrogen loads. Other nitrite-oxidizing bacteria such as Nitrobacter or Nitrotoga were functionally not relevant in the investigated biofilters. Nitrospira-related 16S rRNA gene sequences were obtained from the samples with 10 mM nitrite and analyzed by a cloning approach. Sequence studies revealed four different phylogenetic clusters within the marine sublineage IV of Nitrospira, though most sequences clustered with the type strain of Nitrospira marina and with a strain isolated from a marine RAS. Three lipids dominated the whole fatty acid profiles of nitrite-oxidizing marine and brackish enrichments of Nitrospira sublineage IV organisms. The membranes included two marker lipids (16∶1 cis7 and 16∶1 cis11) combined with the non-specific acid 16∶0 as major compounds and confirmed these marker lipids as characteristic for sublineage IV species. The predominant labeling of these characteristic fatty acids and the phylogenetic sequence analyses of the marine Nitrospira sublineage IV identified organisms of this sublineage as main autotrophic nitrite-oxidizers in the investigated brackish biofilter systems.