Resistant ammonia‐oxidizing archaea endure, but adapting ammonia‐oxidizing bacteria thrive in boreal lake sediments receiving nutrient‐rich effluents

Abstract

SummaryClimate change along with anthropogenic activities changes biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia‐oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the least diverse and least resistant prokaryotic communities from the most wastewater‐influenced sediments, the community changed fast toward the natural composition with the diminishing influence of wastewater. Each lake hosted a unique resistant AOA community, while AOB communities were adapting, responding to environmental conditions as well as receiving new members from WWTPs. In general, AOB dominated in numbers in wastewater‐influenced sediments, while the ratio between AOA and AOB increased when moving toward pristine conditions. Our results suggest that although future climate‐change‐driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities.

Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida)

“…These results agree with those from a previous study in the Gulf of Mexico (Newell et al, 2014), where benthic AOA communities were less diverse following Hurricanes Ike and Gustav, suggesting a weak resistance to disturbance. Increased AOB abundance in our study also supports disturbance studies in boreal lake sediments (Aalto et al, 2018) and estuaries (Happel et al, 2018), where AOB diversity and/or abundance increased at affected sites, suggesting that AOB are more adaptable to disruptive events (Aalto et al, 2018).…”

“…Sequences longer than 555 bp for AOA, and 475 bp for AOB, and low-quality sequences with more than one mismatch in barcode/primer sequences, were removed in Mothur. Frameshift errors in unique archaeal and bacterial reads were corrected using the FunGene FrameBot tool (Wang et al, 2013), and sequence alignment was conducted using aligned archaeal or bacterial amoA sequences retrieved from the FunGene database (Aalto et al, 2018). Chimeric sequences were removed using Uchime in Mothur (Edgar et al, 2011), and sequences were clustered into OTUs at 95% sequence identity.…”

“…The taxonomic assignment of archaeal and bacterial sequences was completed in Mothur using the Alves et al (2018) comprehensive AOA amoA database and custom AOB amoA reference libraries, which were collected from sequences and their taxonomies in the Nucleotide database (Aalto et al, 2018) at a 95% cutoff (Beman and Francis, 2006;Frank et al, 2016;Aalto et al, 2018). Phylogenetic analysis was conducted in MEGA X, where sequences were aligned using the multiple sequence alignment tool, ClustalW, to align representative and reference sequences.…”

Microbial resistance and resilience in response to environmental changes under the higher intensity of human activities than global average level

“…These authors found that ammonia oxidation rates were completely different when AOA activities were dominant over AOB. Aalto et al () also showed that nitrification would be promoted by increasing AOB communities with increases in nutrient loadings in lake ecosystems. Therefore, microbial composition and their abundances were very important to their functional resistance and resilience, and their changes would alter the ecosystem function by changing the process rates.…”

“…Some studies reported that microbial composition was not connected with the prediction of microbial functions so that the composition cannot estimate the microbial resistance and resilience to ecosystem disturbance related to the ecosystem function and service aspects (Nannipieri et al, ; Sjöstedt, Langenheder, Kritzberg, Karlsson, & Lindström, ). However, some researchers have found that microbial composition was very important to the ecosystem processes, especially for the process rates (Aalto, Saarenheimo, Mikkonen, Rissanen, & Tiirola, ; Allison & Martiny, ; Baho, Peter, & Tranvik, ; Galand et al, ). Interestingly, de Vries et al () demonstrated that the bacterial community was not associated with ecosystem respiration under drought conditions, but was directly associated with ecosystem respiration after 1 week of rewetting.…”